[Gmod-gbrowse] Problem with installing GBrowse

[Hufeng Zhou]

Hello:
I have some problem with GBrowse, during the installation it has some
errors so higher versions won't be able to install, I was only able to
install GBrowse-1.66.

I can access http://localhost/gbrowse/ without any problems, and all the
html pages can be viewed, the problem is in the welcome page, it suggest me
to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example data.
But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
accessed, which shows not found error.

I am wondering if it is GBrowse is not running? If there is any way to
resolve this issue? Thanks very much.

After installation,
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

[Scott Cain]

I forgot to cc the GBrowse mailing list; Hufeng, please reply to this email
so it stays on list.

Scott

Hi Hufeng,
Sorry it took so long to get to this message; it was caught in the spam
trap that doesn't allow non-members to post to the list.
Is there a reason you aren't trying to install GBrowse2? GBrowse 1.66 is
extremely old. What were the problems you had?
If you really want to continue with 1.66, please look in the apache access
log to see where apache is looking for the gbrowse cgi script, and then try
to find where it did get installed. Since distros are different with
regard to where they put various files, it can be difficult for me to guess
where they are. One possible suggestion that sometimes trips up new users
is this: if you tried to install GBrowse before you installed apache, the
GBrowse installer may have created a /usr/local/apache directory for you.
If it did, I suggest you remove that directory and reinstall GBrowse.
Scott

Post by Hufeng Zhou
I have some problem with GBrowse, during the installation it has some
errors so higher versions won't be able to install, I was only able to
install GBrowse-1.66.
I can access http://localhost/gbrowse/ without any problems, and all the
html pages can be viewed, the problem is in the welcome page, it suggest me
to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example
data. But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not
be accessed, which shows not found error.
I am wondering if it is GBrowse is not running? If there is any way to
resolve this issue? Thanks very much.
After installation,
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/
------------------------------------------------------------------------------
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

[Scott Cain]

Hi Hufeng,

Please keep this on the GBrowse mailing list (reply-all).

I don't understand why you haven't tried to update the version of
Bio::Graphics first, since the GBrowse installer asked you to install it.

Can you point me to the documentation for ChiA-PET, because I have heard of
people using ChiA-PET data with GBrowse2.

Scott

Thanks very much for your reply.
It is like this, I need to use a package called the ChiA-PET tool that
need to only use GBrowse version 1 (they mentioned on their manual,
version 2 won't work)
So I am trying to install the GBrowse version 1....
If I try to install Version 1.7
I will have following error
Installed Bio::Graphics version 1.654 is less than desired version 1.7.
You probably need to update your BioPerl to version 1.6 or better and
install Bio::Graphics separately from CPAN.
Died at Makefile.PL line 272, <DATA> line 192.
That is why I tried version. 1.66 it is the only package I can
install, but after I install it, I find version 1.66 can not even run
the example data.
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).
I really need your help on this.
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Sorry it took so long to get to this message; it was caught in the spam

trap

that doesn't allow non-members to post to the list.
Is there a reason you aren't trying to install GBrowse2? GBrowse 1.66 is
extremely old. What were the problems you had?
If you really want to continue with 1.66, please look in the apache

access

log to see where apache is looking for the gbrowse cgi script, and then

try

to find where it did get installed. Since distros are different with

regard

to where they put various files, it can be difficult for me to guess

where

they are. One possible suggestion that sometimes trips up new users is
this: if you tried to install GBrowse before you installed apache, the
GBrowse installer may have created a /usr/local/apache directory for you.
If it did, I suggest you remove that directory and reinstall GBrowse.
Scott

Post by Hufeng Zhou
I have some problem with GBrowse, during the installation it has some
errors so higher versions won't be able to install, I was only able to
install GBrowse-1.66.
I can access http://localhost/gbrowse/ without any problems, and all

the

Post by Hufeng Zhou
html pages can be viewed, the problem is in the welcome page, it

suggest me

Post by Hufeng Zhou
to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example

data.

Post by Hufeng Zhou
But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
accessed, which shows not found error.
I am wondering if it is GBrowse is not running? If there is any way to
resolve this issue? Thanks very much.
After installation,
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

------------------------------------------------------------------------------

Post by Hufeng Zhou
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain

dot

net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

[Scott Cain]

Hi Hufeng,

BioPerl and BioGraphics are two different things. I suspect BioPerl from
git will work fine, you must also install BioGraphics, most easily done
with CPAN:

cpan
cpan> install Bio::Graphics

Which will get you the most recent release of BioGraphics. Then you should
be able to install GBrowse 1.70, which is the most recent version of
GBrowse 1 available (though that's still 5 years old).

I imagine the reason you want to use GBrowse 1 is because ChIA-PET creates
a GBrowse configuration file for you, which I suppose is some benefit as
you can't directly use a GBrowse 1 configuration file with GBrowse2. The
data that it generates is (I believe) compatible with GBrowse2 as well as
JBrowse (which is *much* easier to set up).

Scott

Thanks very much for your help.
I use this version of bioperl because,
Packaged versions of BioPerl contain a bug that prevents GBrowse from
displaying DNA sequences from in-memory databases. Install Bioperl
git clone https://github.com/bioperl/bioperl-live.git
cd bioperl-live
perl Build.PL
./Build test
sudo ./Build install
http://gmod.org/wiki/GBrowse_2.0_Prerequisites
And I find most of the bioperl version are quite old, may I know what
is the recommended version? I actually have some problem in installing
the latest version of bioperl but I forced to install the latest
version some how.
You can get the manual of ChiA-pet tool here.
http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Please keep this on the GBrowse mailing list (reply-all).
I don't understand why you haven't tried to update the version of
Bio::Graphics first, since the GBrowse installer asked you to install it.
Can you point me to the documentation for ChiA-PET, because I have heard

of

people using ChiA-PET data with GBrowse2.
Scott

Thanks very much for your reply.
It is like this, I need to use a package called the ChiA-PET tool that
need to only use GBrowse version 1 (they mentioned on their manual,
version 2 won't work)
So I am trying to install the GBrowse version 1....
If I try to install Version 1.7
I will have following error
Installed Bio::Graphics version 1.654 is less than desired version 1.7.
You probably need to update your BioPerl to version 1.6 or better and
install Bio::Graphics separately from CPAN.
Died at Makefile.PL line 272, <DATA> line 192.
That is why I tried version. 1.66 it is the only package I can
install, but after I install it, I find version 1.66 can not even run
the example data.
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).
I really need your help on this.
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Sorry it took so long to get to this message; it was caught in the

spam

trap
that doesn't allow non-members to post to the list.
Is there a reason you aren't trying to install GBrowse2? GBrowse 1.66 is
extremely old. What were the problems you had?
If you really want to continue with 1.66, please look in the apache
access
log to see where apache is looking for the gbrowse cgi script, and

then

try
to find where it did get installed. Since distros are different with
regard
to where they put various files, it can be difficult for me to guess
where
they are. One possible suggestion that sometimes trips up new users

is

this: if you tried to install GBrowse before you installed apache, the
GBrowse installer may have created a /usr/local/apache directory for you.
If it did, I suggest you remove that directory and reinstall GBrowse.
Scott
On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou <

Post by Hufeng Zhou
I have some problem with GBrowse, during the installation it has some
errors so higher versions won't be able to install, I was only able

to

Post by Hufeng Zhou
install GBrowse-1.66.
I can access http://localhost/gbrowse/ without any problems, and all the
html pages can be viewed, the problem is in the welcome page, it suggest me
to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example data.
But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
accessed, which shows not found error.
I am wondering if it is GBrowse is not running? If there is any way

to

Post by Hufeng Zhou
resolve this issue? Thanks very much.
After installation,
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

------------------------------------------------------------------------------

Post by Hufeng Zhou
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--

------------------------------------------------------------------------

Scott Cain, Ph. D. scott at

scottcain

dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain

dot

net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

[Scott Cain]

Hi Hufeng,

Do you have apache installed (or alternatively, did you try to install
GBrowse once before you had apache installed)? The installer rather
annoyingly assumes that if it doesn't find the "standard" locations for
apache directories (which are also annoying different for different
distros), it assumes that you must either have or be planning to have an
apache server that you'll build yourself, which would go in
/usr/local/apache2.

I can't tell from the output you sent what distro you're using, but I
assume that you now have a webserver installed via the distro's package
management software. Assuming that's true, you can delete the
/usr/local/apache2 directory and then try to reinstall GBrowse. One thing
I don't understand is how you have a gbrowse directory in /var/www given
that the installer wants to install in /usr/local/apache2. The fact that
there is also an html directory in /var/www makes me think that the htdocs
directory for the installer should be /var/www/html, something that it will
hopefully guess correctly after you remove the /usr/local/apache2 directory
(though honestly, it may not, since, again, it's an old installer). If I
knew what distro you were using, I could probably suggest the correct
values for those items.

Scott

Thank you very much for your willingness to help.
it looks to be successfully installed, but I can't access the sample data
and can't see the GBrowse visualize the genome,
An example in-memory database from yeast chromosome 1 has been installed
http://localhost/cgi-bin/gbrowse/yeast_chr1
Here localhost/ is the directory on my server,/var/www/
total 8
drwxr-xr-x 10 root root 4096 Sep 1 17:00 gbrowse
drwxr-xr-x 4 root root 4096 Oct 24 17:05 html
but there is no cgi-bin in the directory /var/www/
only apach has in the following directory
/usr/local/apache2/cgi-bin
I am wondering if that is the causes of the issue?
So I need your help on this issue, thanks very much.
Here pasted the detail history of how I install the GBrowse1.70,
Apache root directory (enter '' for none)? [/usr/local/apache2]
Apache conf directory? [/usr/local/apache2/conf]
Apache htdocs directory? [/usr/local/apache2/htdocs]
Apache cgibin directory? [/usr/local/apache2/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths
CONF /usr/local/apache2/conf
HTDOCS /usr/local/apache2/htdocs
CGIBIN /usr/local/apache2/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm
blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm
blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm
blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm
blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm
blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/
allele_tower.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/Synteny.pm
blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm
blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Realign.pm
blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/
connector.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm
blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm
blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/
drosophila_arrow.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm
blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm
blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm
blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm
blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/
match_gap.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Browser/Markup.pm
blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm
blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/
pairwise_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm
blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/
phased_exons.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/
ld_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm
blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp -typemap
/usr/share/perl/5.18/ExtUtils/typemap CAlign.xs > CAlign.xsc && mv
CAlign.xsc CAlign.c
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector
-fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\"
-fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/
process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/
wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS
bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/
process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/
make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
make_das_conf.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/
ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS
cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS
install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS
install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS
install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM"
"-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0,
'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.95 cusr
0.03 csys = 1.01 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture
dependent library tree
Installing /usr/local/lib/perl/5.18.2/CGI/Toggle.pm
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man3/CGI::Toggle.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing /usr/local/bin/make_das_conf.pl
Installing /usr/local/bin/wiggle2gff3.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl"
"CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs"
"CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse"
"APACHE=/usr/local/apache2"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl"
"CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs"
"CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse"
"APACHE=/usr/local/apache2"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache2/cgi-bin/das
copying gbgff to /usr/local/apache2/cgi-bin/gbgff
copying gbrowse to /usr/local/apache2/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache2/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache2/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache2/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache2/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache2/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache2/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
htdocs_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1"
"HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin"
"GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...
#############################################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference
manual.
#############################################################################
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Post by Hufeng Zhou
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.
But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
BioPerl and BioGraphics are two different things. I suspect BioPerl

from

git will work fine, you must also install BioGraphics, most easily done

with

cpan
cpan> install Bio::Graphics
Which will get you the most recent release of BioGraphics. Then you

should

be able to install GBrowse 1.70, which is the most recent version of

GBrowse

1 available (though that's still 5 years old).
I imagine the reason you want to use GBrowse 1 is because ChIA-PET

creates a

GBrowse configuration file for you, which I suppose is some benefit as

you

can't directly use a GBrowse 1 configuration file with GBrowse2. The

data

that it generates is (I believe) compatible with GBrowse2 as well as

JBrowse

(which is *much* easier to set up).
Scott

Thanks very much for your help.
I use this version of bioperl because,
Packaged versions of BioPerl contain a bug that prevents GBrowse from
displaying DNA sequences from in-memory databases. Install Bioperl
git clone https://github.com/bioperl/bioperl-live.git
cd bioperl-live
perl Build.PL
./Build test
sudo ./Build install
http://gmod.org/wiki/GBrowse_2.0_Prerequisites
And I find most of the bioperl version are quite old, may I know what
is the recommended version? I actually have some problem in installing
the latest version of bioperl but I forced to install the latest
version some how.
You can get the manual of ChiA-pet tool here.
http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Please keep this on the GBrowse mailing list (reply-all).
I don't understand why you haven't tried to update the version of
Bio::Graphics first, since the GBrowse installer asked you to install it.
Can you point me to the documentation for ChiA-PET, because I have

heard

of
people using ChiA-PET data with GBrowse2.
Scott
On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <

Thanks very much for your reply.
It is like this, I need to use a package called the ChiA-PET tool

that

need to only use GBrowse version 1 (they mentioned on their manual,
version 2 won't work)
So I am trying to install the GBrowse version 1....
If I try to install Version 1.7
I will have following error
Installed Bio::Graphics version 1.654 is less than desired version

1.7.

You probably need to update your BioPerl to version 1.6 or better

and

install Bio::Graphics separately from CPAN.
Died at Makefile.PL line 272, <DATA> line 192.
That is why I tried version. 1.66 it is the only package I can
install, but after I install it, I find version 1.66 can not even

run

the example data.
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be

accessed).

I really need your help on this.
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Sorry it took so long to get to this message; it was caught in the spam
trap
that doesn't allow non-members to post to the list.
Is there a reason you aren't trying to install GBrowse2? GBrowse
1.66
is
extremely old. What were the problems you had?
If you really want to continue with 1.66, please look in the

apache

access
log to see where apache is looking for the gbrowse cgi script, and then
try
to find where it did get installed. Since distros are different

with

regard
to where they put various files, it can be difficult for me to

guess

where
they are. One possible suggestion that sometimes trips up new

users

is
this: if you tried to install GBrowse before you installed apache, the
GBrowse installer may have created a /usr/local/apache directory

for

you.
If it did, I suggest you remove that directory and reinstall

GBrowse.

Scott
On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou

Post by Hufeng Zhou
I have some problem with GBrowse, during the installation it has some
errors so higher versions won't be able to install, I was only

able

Post by Hufeng Zhou
to
install GBrowse-1.66.
I can access http://localhost/gbrowse/ without any problems,

and all

Post by Hufeng Zhou
the
html pages can be viewed, the problem is in the welcome page, it
suggest me
to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the

example

Post by Hufeng Zhou
data.
But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can

not be

Post by Hufeng Zhou
accessed, which shows not found error.
I am wondering if it is GBrowse is not running? If there is any

way

Post by Hufeng Zhou
to
resolve this issue? Thanks very much.
After installation,
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

------------------------------------------------------------------------------

Post by Hufeng Zhou
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--

------------------------------------------------------------------------

Scott Cain, Ph. D. scott at scottcain
dot
net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Ontario Institute for Cancer Research

--

------------------------------------------------------------------------

Scott Cain, Ph. D. scott at

scottcain

dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain

dot

net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

[Scott Cain]

No--you want apache2. If you have the directory /usr/local/apache or
/usr/local/apache2, delete it and reinstall GBrowse.

Thank you very much indeed for the indepth discussion and help, I am very
grateful.
I actually installed apache2 on this machine already before I install
GBrowse, shall I install apache version 1 instead now? If so, I will
reinstall the apache version 1 and re-install GBrows now.
Our lab is very focus on the ChIA-PET data analysis and I have an
independent Dell Power Edge server to use as my desktop for the ChIA-PET
data analysis so it is not a webserver, but a dedicate powerful desktop. I
use the Ubuntu distro version 14.10. I will try to install Apache1. at the
moment.
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Do you have apache installed (or alternatively, did you try to install
GBrowse once before you had apache installed)? The installer rather
annoyingly assumes that if it doesn't find the "standard" locations for
apache directories (which are also annoying different for different
distros), it assumes that you must either have or be planning to have an
apache server that you'll build yourself, which would go in
/usr/local/apache2.
I can't tell from the output you sent what distro you're using, but I
assume that you now have a webserver installed via the distro's package
management software. Assuming that's true, you can delete the
/usr/local/apache2 directory and then try to reinstall GBrowse. One thing
I don't understand is how you have a gbrowse directory in /var/www given
that the installer wants to install in /usr/local/apache2. The fact that
there is also an html directory in /var/www makes me think that the htdocs
directory for the installer should be /var/www/html, something that it will
hopefully guess correctly after you remove the /usr/local/apache2 directory
(though honestly, it may not, since, again, it's an old installer). If I
knew what distro you were using, I could probably suggest the correct
values for those items.
Scott

Thank you very much for your willingness to help.
it looks to be successfully installed, but I can't access the sample
data and can't see the GBrowse visualize the genome,
An example in-memory database from yeast chromosome 1 has been installed
http://localhost/cgi-bin/gbrowse/yeast_chr1
Here localhost/ is the directory on my server,/var/www/
total 8
drwxr-xr-x 10 root root 4096 Sep 1 17:00 gbrowse
drwxr-xr-x 4 root root 4096 Oct 24 17:05 html
but there is no cgi-bin in the directory /var/www/
only apach has in the following directory
/usr/local/apache2/cgi-bin
I am wondering if that is the causes of the issue?
So I need your help on this issue, thanks very much.
Here pasted the detail history of how I install the GBrowse1.70,
Apache root directory (enter '' for none)? [/usr/local/apache2]
Apache conf directory? [/usr/local/apache2/conf]
Apache htdocs directory? [/usr/local/apache2/htdocs]
Apache cgibin directory? [/usr/local/apache2/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths
CONF /usr/local/apache2/conf
HTDOCS /usr/local/apache2/htdocs
CGIBIN /usr/local/apache2/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm
blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm
blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm
blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm
blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm
blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/
allele_tower.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/Synteny.pm
blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm
blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/
orf.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Realign.pm
blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/
connector.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm
blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm
blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm
blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm
blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm
blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm
blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm
blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm
blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Browser/Markup.pm
blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm
blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/
pairwise_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm
blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/
salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/
phased_exons.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/
ld_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm
blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp -typemap
/usr/share/perl/5.18/ExtUtils/typemap CAlign.xs > CAlign.xsc && mv
CAlign.xsc CAlign.c
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector
-fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\"
-fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/
process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/
wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS
bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/
process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/
make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
make_das_conf.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/
ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS
cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS
install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS
install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS
install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM"
"-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0,
'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.95 cusr
0.03 csys = 1.01 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture
dependent library tree
Installing /usr/local/lib/perl/5.18.2/CGI/Toggle.pm
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man3/CGI::Toggle.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing /usr/local/bin/make_das_conf.pl
Installing /usr/local/bin/wiggle2gff3.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
conf_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1"
"HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin"
"GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl"
"CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs"
"CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse"
"APACHE=/usr/local/apache2"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache2/cgi-bin/das
copying gbgff to /usr/local/apache2/cgi-bin/gbgff
copying gbrowse to /usr/local/apache2/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache2/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache2/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache2/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache2/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache2/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache2/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
htdocs_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1"
"HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin"
"GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...
#############################################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference
manual.
#############################################################################
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Post by Hufeng Zhou
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.
But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
BioPerl and BioGraphics are two different things. I suspect BioPerl

from

git will work fine, you must also install BioGraphics, most easily

done with

cpan
cpan> install Bio::Graphics
Which will get you the most recent release of BioGraphics. Then you

should

be able to install GBrowse 1.70, which is the most recent version of

GBrowse

1 available (though that's still 5 years old).
I imagine the reason you want to use GBrowse 1 is because ChIA-PET

creates a

GBrowse configuration file for you, which I suppose is some benefit

as you

can't directly use a GBrowse 1 configuration file with GBrowse2. The

data

that it generates is (I believe) compatible with GBrowse2 as well as

JBrowse

(which is *much* easier to set up).
Scott
On Tue, Nov 11, 2014 at 5:08 PM, Hufeng Zhou <

Thanks very much for your help.
I use this version of bioperl because,
Packaged versions of BioPerl contain a bug that prevents GBrowse from
displaying DNA sequences from in-memory databases. Install Bioperl
git clone https://github.com/bioperl/bioperl-live.git
cd bioperl-live
perl Build.PL
./Build test
sudo ./Build install
http://gmod.org/wiki/GBrowse_2.0_Prerequisites
And I find most of the bioperl version are quite old, may I know what
is the recommended version? I actually have some problem in

installing

the latest version of bioperl but I forced to install the latest
version some how.
You can get the manual of ChiA-pet tool here.
http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Please keep this on the GBrowse mailing list (reply-all).
I don't understand why you haven't tried to update the version of
Bio::Graphics first, since the GBrowse installer asked you to

install

it.
Can you point me to the documentation for ChiA-PET, because I have

heard

of
people using ChiA-PET data with GBrowse2.
Scott
On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <

Thanks very much for your reply.
It is like this, I need to use a package called the ChiA-PET tool

that

need to only use GBrowse version 1 (they mentioned on their

manual,

version 2 won't work)
So I am trying to install the GBrowse version 1....
If I try to install Version 1.7
I will have following error
Installed Bio::Graphics version 1.654 is less than desired

version 1.7.

You probably need to update your BioPerl to version 1.6 or better

and

install Bio::Graphics separately from CPAN.
Died at Makefile.PL line 272, <DATA> line 192.
That is why I tried version. 1.66 it is the only package I can
install, but after I install it, I find version 1.66 can not even

run

the example data.
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be

accessed).

I really need your help on this.
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Sorry it took so long to get to this message; it was caught in

the

spam
trap
that doesn't allow non-members to post to the list.
Is there a reason you aren't trying to install GBrowse2?

GBrowse

1.66
is
extremely old. What were the problems you had?
If you really want to continue with 1.66, please look in the

apache

access
log to see where apache is looking for the gbrowse cgi script,

and

then
try
to find where it did get installed. Since distros are

different with

regard
to where they put various files, it can be difficult for me to

guess

where
they are. One possible suggestion that sometimes trips up new

users

is
this: if you tried to install GBrowse before you installed

apache,

the
GBrowse installer may have created a /usr/local/apache

directory for

you.
If it did, I suggest you remove that directory and reinstall

GBrowse.

Scott
On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou

Post by Hufeng Zhou
I have some problem with GBrowse, during the installation it

has

Post by Hufeng Zhou
some
errors so higher versions won't be able to install, I was only

able

Post by Hufeng Zhou
to
install GBrowse-1.66.
I can access http://localhost/gbrowse/ without any problems,

and all

Post by Hufeng Zhou
the
html pages can be viewed, the problem is in the welcome page,

it

Post by Hufeng Zhou
suggest me
to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the

example

Post by Hufeng Zhou
data.
But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can

not be

Post by Hufeng Zhou
accessed, which shows not found error.
I am wondering if it is GBrowse is not running? If there is

any way

Post by Hufeng Zhou
to
resolve this issue? Thanks very much.
After installation,
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

------------------------------------------------------------------------------

Post by Hufeng Zhou
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--

------------------------------------------------------------------------

Scott Cain, Ph. D. scott at
scottcain
dot
net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Ontario Institute for Cancer Research

--

------------------------------------------------------------------------

Scott Cain, Ph. D. scott at

scottcain

dot
net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Ontario Institute for Cancer Research

--

------------------------------------------------------------------------

Scott Cain, Ph. D. scott at

scottcain dot

net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

[Scott Cain]

Hi Hufeng,

Does /usr/lib/cgi-bin exist (which is where , and is the a file called
gbrowse in it?

I find the precious package in /var/www/html/gbrowse/ was old one, didn't
updated since my last installation in Oct.
So I did delete both /usr/local/apache or /usr/local/apache2 and
/var/www/html/gbrowse/
And now I have unpack the GBrowse 1.70 and try the installation all from
the very beginning, but the problem persists with the following history,
I still can't access the example data at
http://localhost/cgi-bin/gbrowse/yeast
which always shows
The requested URL /cgi-bin/gbrowse/yeast was not found on this server.
------------------------------
Apache/2.4.7 (Ubuntu) Server at localhost Port 80
Should I use your previous settings to set the file paths and options
(y/n) [y]? n
Apache root directory (enter '' for none)?
Apache conf directory? [/etc/apache2]
Apache htdocs directory? [/var/www/html]
Apache cgibin directory? [/usr/lib/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths
CONF /etc/apache2
HTDOCS /var/www/html
CGIBIN /usr/lib/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
Skip blib/lib/Bio/Graphics/Browser/I18n.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyBlock.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Realign.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm (unchanged)
Skip blib/lib/Bio/Graphics/DenseFeature.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/OptionPick.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PluginSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/allele_tower.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/GFFhelper.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/connector.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Markup.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Plugin.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PadAlignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PageSettings.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Synteny.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Util.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/UploadSet.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyIO.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/orf.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/ld_plot.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/phased_exons.pm (unchanged)
Skip blib/lib/CGI/Session/ID/salted_md5.pm (unchanged)
Skip blib/lib/Bio/Graphics/WiggleBlockFile.pm (unchanged)
Skip blib/lib/CGI/Toggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm (unchanged)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Skip ../blib/lib/Bio/Graphics/Browser/CAlign.pm (unchanged)
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector
-fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\"
-fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/
process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/
process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/
make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/
wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS
bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
register_moby_services.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/
ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS
cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS
install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS
install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS
install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM"
"-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0,
'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.91 cusr
0.08 csys = 1.02 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture
dependent library tree
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl"
"CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2"
"GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl"
"CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2"
"GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/lib/cgi-bin/das
copying gbgff to /usr/lib/cgi-bin/gbgff
copying gbrowse to /usr/lib/cgi-bin/gbrowse
copying gbrowse_details to /usr/lib/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/lib/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/lib/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/lib/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/lib/cgi-bin/gbrowse_syn
copying moby_server to /usr/lib/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
htdocs_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html"
"CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing stylesheet and images...
Making /var/www/html/gbrowse/images...
Making /var/www/html/gbrowse/images/buttons...
Making /var/www/html/gbrowse/images/balloons...
Making /var/www/html/gbrowse/js...
Making /var/www/html/gbrowse/images/help...
Installing temporary directory...
Making /var/www/html/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...
#############################################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference
manual.
#############################################################################
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Thanks very much, I deleted the /usr/local/apache2
but the problem persist, I still can not access the exemplary data here.
http://localhost/cgi-bin/gbrowse/yeast_chr1
Apache root directory (enter '' for none)? [/usr/local/apache] ''
Apache conf directory? [/usr/local/apache/conf]
Apache htdocs directory? [/usr/local/apache/htdocs]
Apache cgibin directory? [/usr/local/apache/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths
CONF /usr/local/apache/conf
HTDOCS /usr/local/apache/htdocs
CGIBIN /usr/local/apache/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/
allele_tower.pm
cp lib/Bio/Graphics/Browser/Synteny.pm
blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm
blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm
blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm
blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm
blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm
blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/
connector.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm
blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/Graphics/Browser/Realign.pm
blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm
blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm
blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm
blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm
blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/
match_gap.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Markup.pm
blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm
blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm
blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm
blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/
phased_exons.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/
pairwise_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm
blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/
ld_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm
blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm
blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp -typemap
/usr/share/perl/5.18/ExtUtils/typemap CAlign.xs > CAlign.xsc && mv
CAlign.xsc CAlign.c
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector
-fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\"
-fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/
wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/
process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS
bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/
make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/
process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_wormbase.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/
ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS
cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS
install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS
install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS
install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM"
"-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0,
'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 2 wallclock secs ( 0.03 usr 0.00 sys + 0.98 cusr
0.07 csys = 1.08 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture
dependent library tree
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man1/process_wormbase.pl.1p
Installing /usr/local/man/man1/make_das_conf.pl.1p
Installing /usr/local/man/man1/process_sgd.pl.1p
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl"
"APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf"
"CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs"
"DO_XS=1"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl"
"APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf"
"CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs"
"DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache/cgi-bin/das
copying gbgff to /usr/local/apache/cgi-bin/gbgff
copying gbrowse to /usr/local/apache/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
htdocs_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse"
"CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin"
"HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing stylesheet and images...
Making /usr/local/apache/htdocs/gbrowse/images...
Making /usr/local/apache/htdocs/gbrowse/images/buttons...
Making /usr/local/apache/htdocs/gbrowse/images/balloons...
Making /usr/local/apache/htdocs/gbrowse/js...
Making /usr/local/apache/htdocs/gbrowse/images/help...
Installing temporary directory...
Making /usr/local/apache/htdocs/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...
#############################################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference
manual.
#############################################################################
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Post by Scott Cain
No--you want apache2. If you have the directory /usr/local/apache or
/usr/local/apache2, delete it and reinstall GBrowse.

Thank you very much indeed for the indepth discussion and help, I am
very grateful.
I actually installed apache2 on this machine already before I install
GBrowse, shall I install apache version 1 instead now? If so, I will
reinstall the apache version 1 and re-install GBrows now.
Our lab is very focus on the ChIA-PET data analysis and I have an
independent Dell Power Edge server to use as my desktop for the ChIA-PET
data analysis so it is not a webserver, but a dedicate powerful desktop. I
use the Ubuntu distro version 14.10. I will try to install Apache1. at the
moment.
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Do you have apache installed (or alternatively, did you try to install
GBrowse once before you had apache installed)? The installer rather
annoyingly assumes that if it doesn't find the "standard" locations for
apache directories (which are also annoying different for different
distros), it assumes that you must either have or be planning to have an
apache server that you'll build yourself, which would go in
/usr/local/apache2.
I can't tell from the output you sent what distro you're using, but I
assume that you now have a webserver installed via the distro's package
management software. Assuming that's true, you can delete the
/usr/local/apache2 directory and then try to reinstall GBrowse. One thing
I don't understand is how you have a gbrowse directory in /var/www given
that the installer wants to install in /usr/local/apache2. The fact that
there is also an html directory in /var/www makes me think that the htdocs
directory for the installer should be /var/www/html, something that it will
hopefully guess correctly after you remove the /usr/local/apache2 directory
(though honestly, it may not, since, again, it's an old installer). If I
knew what distro you were using, I could probably suggest the correct
values for those items.
Scott

Thank you very much for your willingness to help.
it looks to be successfully installed, but I can't access the sample
data and can't see the GBrowse visualize the genome,
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1
Here localhost/ is the directory on my server,/var/www/
total 8
drwxr-xr-x 10 root root 4096 Sep 1 17:00 gbrowse
drwxr-xr-x 4 root root 4096 Oct 24 17:05 html
but there is no cgi-bin in the directory /var/www/
only apach has in the following directory
/usr/local/apache2/cgi-bin
I am wondering if that is the causes of the issue?
So I need your help on this issue, thanks very much.
Here pasted the detail history of how I install the GBrowse1.70,
Apache root directory (enter '' for none)? [/usr/local/apache2]
Apache conf directory? [/usr/local/apache2/conf]
Apache htdocs directory? [/usr/local/apache2/htdocs]
Apache cgibin directory? [/usr/local/apache2/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths
CONF /usr/local/apache2/conf
HTDOCS /usr/local/apache2/htdocs
CGIBIN /usr/local/apache2/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm
blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm
blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm
blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm
blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm
blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/Graphics/Glyph/allele_tower.pm
blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/Synteny.pm
blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/Graphics/DenseFeature.pm
blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm
blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/
orf.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Realign.pm
blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser/Util.pm
blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/
connector.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm
blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm
blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm
blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm
blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm
blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm
blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm
blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/I18n.pm
blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm
blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Browser/Markup.pm
blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm
blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm
blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm
blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/
salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm
blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/
ld_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm
blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp -typemap
/usr/share/perl/5.18/ExtUtils/typemap CAlign.xs > CAlign.xsc && mv
CAlign.xsc CAlign.c
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector
-fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\"
-fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/
process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/
wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable
substitutions)
cp bin/register_moby_services.pl blib/script/
register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/
process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/
make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
make_das_conf.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/
ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS
cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS
install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/gbrowse_ppm_install.PLS install_util/
gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM"
"-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0,
'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.95
cusr 0.03 csys = 1.01 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into
architecture dependent library tree
Installing /usr/local/lib/perl/5.18.2/CGI/Toggle.pm
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man3/CGI::Toggle.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing /usr/local/bin/make_das_conf.pl
Installing /usr/local/bin/wiggle2gff3.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
conf_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1"
"HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin"
"GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
cgi_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1"
"HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin"
"GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache2/cgi-bin/das
copying gbgff to /usr/local/apache2/cgi-bin/gbgff
copying gbrowse to /usr/local/apache2/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache2/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache2/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache2/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache2/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache2/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache2/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
htdocs_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1"
"HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin"
"GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...
#############################################################################
GBrowse is now installed. Read INSTALL for further setup
instructions.
Go to http://localhost/gbrowse for the online tutorial and reference
manual.
#############################################################################
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/
On Wed, Nov 12, 2014 at 1:23 PM, Hufeng Zhou <

Post by Hufeng Zhou
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.
But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
BioPerl and BioGraphics are two different things. I suspect

BioPerl from

git will work fine, you must also install BioGraphics, most easily

done with

cpan
cpan> install Bio::Graphics
Which will get you the most recent release of BioGraphics. Then

you should

be able to install GBrowse 1.70, which is the most recent version

of GBrowse

1 available (though that's still 5 years old).
I imagine the reason you want to use GBrowse 1 is because ChIA-PET

creates a

GBrowse configuration file for you, which I suppose is some

benefit as you

can't directly use a GBrowse 1 configuration file with GBrowse2.

The data

that it generates is (I believe) compatible with GBrowse2 as well

as JBrowse

(which is *much* easier to set up).
Scott
On Tue, Nov 11, 2014 at 5:08 PM, Hufeng Zhou <

Thanks very much for your help.
I use this version of bioperl because,
Packaged versions of BioPerl contain a bug that prevents GBrowse

from

displaying DNA sequences from in-memory databases. Install Bioperl
git clone https://github.com/bioperl/bioperl-live.git
cd bioperl-live
perl Build.PL
./Build test
sudo ./Build install
http://gmod.org/wiki/GBrowse_2.0_Prerequisites
And I find most of the bioperl version are quite old, may I know

what

is the recommended version? I actually have some problem in

installing

the latest version of bioperl but I forced to install the latest
version some how.
You can get the manual of ChiA-pet tool here.
http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Please keep this on the GBrowse mailing list (reply-all).
I don't understand why you haven't tried to update the version

of

Bio::Graphics first, since the GBrowse installer asked you to

install

it.
Can you point me to the documentation for ChiA-PET, because I

have heard

of
people using ChiA-PET data with GBrowse2.
Scott
On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <

Thanks very much for your reply.
It is like this, I need to use a package called the ChiA-PET

tool that

need to only use GBrowse version 1 (they mentioned on their

manual,

version 2 won't work)
So I am trying to install the GBrowse version 1....
If I try to install Version 1.7
I will have following error
Installed Bio::Graphics version 1.654 is less than desired

version 1.7.

You probably need to update your BioPerl to version 1.6 or

better and

install Bio::Graphics separately from CPAN.
Died at Makefile.PL line 272, <DATA> line 192.
That is why I tried version. 1.66 it is the only package I can
install, but after I install it, I find version 1.66 can not

even run

the example data.
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be

accessed).

I really need your help on this.
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/
On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <

Hi Hufeng,
Sorry it took so long to get to this message; it was caught

in the

spam
trap
that doesn't allow non-members to post to the list.
Is there a reason you aren't trying to install GBrowse2?

GBrowse

1.66
is
extremely old. What were the problems you had?
If you really want to continue with 1.66, please look in the

apache

access
log to see where apache is looking for the gbrowse cgi

script, and

then
try
to find where it did get installed. Since distros are

different with

regard
to where they put various files, it can be difficult for me

to guess

where
they are. One possible suggestion that sometimes trips up

new users

is
this: if you tried to install GBrowse before you installed

apache,

the
GBrowse installer may have created a /usr/local/apache

directory for

you.
If it did, I suggest you remove that directory and reinstall

GBrowse.

Scott
On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou

Post by Hufeng Zhou
I have some problem with GBrowse, during the installation

it has

Post by Hufeng Zhou
some
errors so higher versions won't be able to install, I was

only able

Post by Hufeng Zhou
to
install GBrowse-1.66.
I can access http://localhost/gbrowse/ without any

problems, and all

Post by Hufeng Zhou
the
html pages can be viewed, the problem is in the welcome

page, it

Post by Hufeng Zhou
suggest me
to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for

the example

Post by Hufeng Zhou
data.
But this link http://localhost/cgi-bin/gbrowse/yeast_chr1

can not be

Post by Hufeng Zhou
accessed, which shows not found error.
I am wondering if it is GBrowse is not running? If there is

any way

Post by Hufeng Zhou
to
resolve this issue? Thanks very much.
After installation,
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

------------------------------------------------------------------------------

Post by Hufeng Zhou
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--

------------------------------------------------------------------------

Scott Cain, Ph. D. scott at
scottcain
dot
net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Ontario Institute for Cancer Research

--

------------------------------------------------------------------------

Scott Cain, Ph. D. scott at

scottcain

dot
net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Ontario Institute for Cancer Research

--

------------------------------------------------------------------------

Scott Cain, Ph. D. scott at

scottcain dot

net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at
scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

[Hufeng Zhou]

Dear Scott:
Thanks very much,
Yeah, indeed /usr/lib/cgi-bin exist as below.

***@kiefflab-cloud:~/Programs/ChIA-PET-tool/pipeline$ ls -l
/usr/lib/cgi-bin
total 348
-rwxr-xr-x 1 root root 35862 Nov 13 12:40 das
-rwxr-xr-x 1 root root 9232 Nov 13 12:40 gbgff
-rwxrwxrwx 1 root root 125875 Nov 13 12:40 gbrowse
-rwxr-xr-x 1 root root 15751 Nov 13 12:40 gbrowse_details
-rwxr-xr-x 1 root root 4562 Nov 13 12:40 gbrowse_est
-rwxr-xr-x 1 root root 35703 Nov 13 12:40 gbrowse_img
-rwxr-xr-x 1 root root 49935 Nov 13 12:40 gbrowse_moby
-rwxr-xr-x 1 root root 51716 Nov 13 12:40 gbrowse_syn
-rwxr-xr-x 1 root root 905 Nov 13 12:40 moby_server
-rwxr-xr-x 1 root root 4166 Sep 1 17:00 tutorial_test.pl


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Does /usr/lib/cgi-bin exist (which is where , and is the a file called
gbrowse in it?

I find the precious package in /var/www/html/gbrowse/ was old one, didn't
updated since my last installation in Oct.
So I did delete both /usr/local/apache or /usr/local/apache2 and
/var/www/html/gbrowse/
And now I have unpack the GBrowse 1.70 and try the installation all from
the very beginning, but the problem persists with the following history,
I still can't access the example data at
http://localhost/cgi-bin/gbrowse/yeast
which always shows
The requested URL /cgi-bin/gbrowse/yeast was not found on this server.
------------------------------
Apache/2.4.7 (Ubuntu) Server at localhost Port 80
Should I use your previous settings to set the file paths and options
(y/n) [y]? n
Apache root directory (enter '' for none)?
Apache conf directory? [/etc/apache2]
Apache htdocs directory? [/var/www/html]
Apache cgibin directory? [/usr/lib/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths
CONF /etc/apache2
HTDOCS /var/www/html
CGIBIN /usr/lib/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
Skip blib/lib/Bio/Graphics/Browser/I18n.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyBlock.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Realign.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm (unchanged)
Skip blib/lib/Bio/Graphics/DenseFeature.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/OptionPick.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PluginSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/allele_tower.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/GFFhelper.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/connector.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Markup.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Plugin.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PadAlignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PageSettings.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Synteny.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Util.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/UploadSet.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyIO.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/orf.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/ld_plot.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/phased_exons.pm (unchanged)
Skip blib/lib/CGI/Session/ID/salted_md5.pm (unchanged)
Skip blib/lib/Bio/Graphics/WiggleBlockFile.pm (unchanged)
Skip blib/lib/CGI/Toggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm (unchanged)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Skip ../blib/lib/Bio/Graphics/Browser/CAlign.pm (unchanged)
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector
-fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\"
-fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/
process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/
process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/
make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/
wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS
bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
register_moby_services.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/
ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS
cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS
install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS
install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS
install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM"
"-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0,
'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.91 cusr
0.08 csys = 1.02 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture
dependent library tree
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl"
"CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2"
"GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl"
"CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2"
"GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/lib/cgi-bin/das
copying gbgff to /usr/lib/cgi-bin/gbgff
copying gbrowse to /usr/lib/cgi-bin/gbrowse
copying gbrowse_details to /usr/lib/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/lib/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/lib/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/lib/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/lib/cgi-bin/gbrowse_syn
copying moby_server to /usr/lib/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
htdocs_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html"
"CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing stylesheet and images...
Making /var/www/html/gbrowse/images...
Making /var/www/html/gbrowse/images/buttons...
Making /var/www/html/gbrowse/images/balloons...
Making /var/www/html/gbrowse/js...
Making /var/www/html/gbrowse/images/help...
Installing temporary directory...
Making /var/www/html/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...
#############################################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference
manual.
#############################################################################
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Thanks very much, I deleted the /usr/local/apache2
but the problem persist, I still can not access the exemplary data here.
http://localhost/cgi-bin/gbrowse/yeast_chr1
Apache root directory (enter '' for none)? [/usr/local/apache] ''
Apache conf directory? [/usr/local/apache/conf]
Apache htdocs directory? [/usr/local/apache/htdocs]
Apache cgibin directory? [/usr/local/apache/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths
CONF /usr/local/apache/conf
HTDOCS /usr/local/apache/htdocs
CGIBIN /usr/local/apache/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/
allele_tower.pm
cp lib/Bio/Graphics/Browser/Synteny.pm
blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm
blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm
blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm
blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm
blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm
blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/
connector.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm
blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/Graphics/Browser/Realign.pm
blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/
orf.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm
blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm
blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm
blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm
blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm
blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Markup.pm
blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm
blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm
blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm
blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/
salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/
phased_exons.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/
pairwise_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm
blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/
ld_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm
blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm
blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp -typemap
/usr/share/perl/5.18/ExtUtils/typemap CAlign.xs > CAlign.xsc && mv
CAlign.xsc CAlign.c
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector
-fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\"
-fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/
wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/
process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS
bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/
make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/
process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_wormbase.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/
ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS
cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS
install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS
install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS
install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM"
"-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0,
'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 2 wallclock secs ( 0.03 usr 0.00 sys + 0.98 cusr
0.07 csys = 1.08 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture
dependent library tree
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man1/process_wormbase.pl.1p
Installing /usr/local/man/man1/make_das_conf.pl.1p
Installing /usr/local/man/man1/process_sgd.pl.1p
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
conf_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse"
"CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin"
"HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl"
"APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf"
"CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs"
"DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache/cgi-bin/das
copying gbgff to /usr/local/apache/cgi-bin/gbgff
copying gbrowse to /usr/local/apache/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
htdocs_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse"
"CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin"
"HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing stylesheet and images...
Making /usr/local/apache/htdocs/gbrowse/images...
Making /usr/local/apache/htdocs/gbrowse/images/buttons...
Making /usr/local/apache/htdocs/gbrowse/images/balloons...
Making /usr/local/apache/htdocs/gbrowse/js...
Making /usr/local/apache/htdocs/gbrowse/images/help...
Installing temporary directory...
Making /usr/local/apache/htdocs/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...
#############################################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference
manual.
#############################################################################
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Post by Scott Cain
No--you want apache2. If you have the directory /usr/local/apache or
/usr/local/apache2, delete it and reinstall GBrowse.

Thank you very much indeed for the indepth discussion and help, I am
very grateful.
I actually installed apache2 on this machine already before I install
GBrowse, shall I install apache version 1 instead now? If so, I will
reinstall the apache version 1 and re-install GBrows now.
Our lab is very focus on the ChIA-PET data analysis and I have an
independent Dell Power Edge server to use as my desktop for the ChIA-PET
data analysis so it is not a webserver, but a dedicate powerful desktop. I
use the Ubuntu distro version 14.10. I will try to install Apache1. at the
moment.
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Do you have apache installed (or alternatively, did you try to
install GBrowse once before you had apache installed)? The installer
rather annoyingly assumes that if it doesn't find the "standard" locations
for apache directories (which are also annoying different for different
distros), it assumes that you must either have or be planning to have an
apache server that you'll build yourself, which would go in
/usr/local/apache2.
I can't tell from the output you sent what distro you're using, but I
assume that you now have a webserver installed via the distro's package
management software. Assuming that's true, you can delete the
/usr/local/apache2 directory and then try to reinstall GBrowse. One thing
I don't understand is how you have a gbrowse directory in /var/www given
that the installer wants to install in /usr/local/apache2. The fact that
there is also an html directory in /var/www makes me think that the htdocs
directory for the installer should be /var/www/html, something that it will
hopefully guess correctly after you remove the /usr/local/apache2 directory
(though honestly, it may not, since, again, it's an old installer). If I
knew what distro you were using, I could probably suggest the correct
values for those items.
Scott
On Wed, Nov 12, 2014 at 1:36 PM, Hufeng Zhou <

Thank you very much for your willingness to help.
it looks to be successfully installed, but I can't access the sample
data and can't see the GBrowse visualize the genome,
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1
Here localhost/ is the directory on my server,/var/www/
total 8
drwxr-xr-x 10 root root 4096 Sep 1 17:00 gbrowse
drwxr-xr-x 4 root root 4096 Oct 24 17:05 html
but there is no cgi-bin in the directory /var/www/
only apach has in the following directory
/usr/local/apache2/cgi-bin
I am wondering if that is the causes of the issue?
So I need your help on this issue, thanks very much.
Here pasted the detail history of how I install the GBrowse1.70,
Apache root directory (enter '' for none)? [/usr/local/apache2]
Apache conf directory? [/usr/local/apache2/conf]
Apache htdocs directory? [/usr/local/apache2/htdocs]
Apache cgibin directory? [/usr/local/apache2/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths
CONF /usr/local/apache2/conf
HTDOCS /usr/local/apache2/htdocs
CGIBIN /usr/local/apache2/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm
blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm
blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm
blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm
blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm
blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/Graphics/Glyph/allele_tower.pm
blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/Synteny.pm
blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/Graphics/DenseFeature.pm
blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm
blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/
orf.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Realign.pm
blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser/Util.pm
blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/
connector.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm
blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm
blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm
blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm
blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm
blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm
blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm
blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/I18n.pm
blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm
blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Browser/Markup.pm
blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm
blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm
blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm
blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/
salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm
blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/
ld_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm
blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp -typemap
/usr/share/perl/5.18/ExtUtils/typemap CAlign.xs > CAlign.xsc && mv
CAlign.xsc CAlign.c
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector
-fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\"
-fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/
process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/
wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable
substitutions)
cp bin/register_moby_services.pl blib/script/
register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS
bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/
make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
make_das_conf.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/
ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS
cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/gbrowse_ppm_install.PLS install_util/
gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM"
"-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0,
'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.95
cusr 0.03 csys = 1.01 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into
architecture dependent library tree
Installing /usr/local/lib/perl/5.18.2/CGI/Toggle.pm
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man3/CGI::Toggle.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing /usr/local/bin/make_das_conf.pl
Installing /usr/local/bin/wiggle2gff3.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
conf_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1"
"HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin"
"GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
cgi_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1"
"HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin"
"GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache2/cgi-bin/das
copying gbgff to /usr/local/apache2/cgi-bin/gbgff
copying gbrowse to /usr/local/apache2/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache2/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache2/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache2/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache2/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache2/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache2/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
htdocs_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1"
"HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin"
"GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement
path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement
path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...
#############################################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and
reference manual.
#############################################################################
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/
On Wed, Nov 12, 2014 at 1:23 PM, Hufeng Zhou <

Post by Hufeng Zhou
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.
But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
BioPerl and BioGraphics are two different things. I suspect

BioPerl from

git will work fine, you must also install BioGraphics, most

easily done with

cpan
cpan> install Bio::Graphics
Which will get you the most recent release of BioGraphics. Then

you should

be able to install GBrowse 1.70, which is the most recent version

of GBrowse

1 available (though that's still 5 years old).
I imagine the reason you want to use GBrowse 1 is because

ChIA-PET creates a

GBrowse configuration file for you, which I suppose is some

benefit as you

can't directly use a GBrowse 1 configuration file with GBrowse2.

The data

that it generates is (I believe) compatible with GBrowse2 as well

as JBrowse

(which is *much* easier to set up).
Scott
On Tue, Nov 11, 2014 at 5:08 PM, Hufeng Zhou <

Thanks very much for your help.
I use this version of bioperl because,
Packaged versions of BioPerl contain a bug that prevents GBrowse

from

displaying DNA sequences from in-memory databases. Install

Bioperl

git clone https://github.com/bioperl/bioperl-live.git
cd bioperl-live
perl Build.PL
./Build test
sudo ./Build install
http://gmod.org/wiki/GBrowse_2.0_Prerequisites
And I find most of the bioperl version are quite old, may I know

what

is the recommended version? I actually have some problem in

installing

the latest version of bioperl but I forced to install the latest
version some how.
You can get the manual of ChiA-pet tool here.
http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Please keep this on the GBrowse mailing list (reply-all).
I don't understand why you haven't tried to update the version

of

Bio::Graphics first, since the GBrowse installer asked you to

install

it.
Can you point me to the documentation for ChiA-PET, because I

have heard

of
people using ChiA-PET data with GBrowse2.
Scott
On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <

Thanks very much for your reply.
It is like this, I need to use a package called the ChiA-PET

tool that

need to only use GBrowse version 1 (they mentioned on their

manual,

version 2 won't work)
So I am trying to install the GBrowse version 1....
If I try to install Version 1.7
I will have following error
Installed Bio::Graphics version 1.654 is less than desired

version 1.7.

You probably need to update your BioPerl to version 1.6 or

better and

install Bio::Graphics separately from CPAN.
Died at Makefile.PL line 272, <DATA> line 192.
That is why I tried version. 1.66 it is the only package I can
install, but after I install it, I find version 1.66 can not

even run

the example data.
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be

accessed).

I really need your help on this.
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/
On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <

Hi Hufeng,
Sorry it took so long to get to this message; it was caught

in the

spam
trap
that doesn't allow non-members to post to the list.
Is there a reason you aren't trying to install GBrowse2?

GBrowse

1.66
is
extremely old. What were the problems you had?
If you really want to continue with 1.66, please look in

the apache

access
log to see where apache is looking for the gbrowse cgi

script, and

then
try
to find where it did get installed. Since distros are

different with

regard
to where they put various files, it can be difficult for me

to guess

where
they are. One possible suggestion that sometimes trips up

new users

is
this: if you tried to install GBrowse before you installed

apache,

the
GBrowse installer may have created a /usr/local/apache

directory for

you.
If it did, I suggest you remove that directory and

reinstall GBrowse.

Scott
On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou

Post by Hufeng Zhou
I have some problem with GBrowse, during the installation

it has

Post by Hufeng Zhou
some
errors so higher versions won't be able to install, I was

only able

Post by Hufeng Zhou
to
install GBrowse-1.66.
I can access http://localhost/gbrowse/ without any

problems, and all

Post by Hufeng Zhou
the
html pages can be viewed, the problem is in the welcome

page, it

Post by Hufeng Zhou
suggest me
to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for

the example

Post by Hufeng Zhou
data.
But this link http://localhost/cgi-bin/gbrowse/yeast_chr1

can not be

Post by Hufeng Zhou
accessed, which shows not found error.
I am wondering if it is GBrowse is not running? If there

is any way

Post by Hufeng Zhou
to
resolve this issue? Thanks very much.
After installation,
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

------------------------------------------------------------------------------

Post by Hufeng Zhou
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--

------------------------------------------------------------------------

Scott Cain, Ph. D. scott

at

scottcain
dot
net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Ontario Institute for Cancer Research

--

------------------------------------------------------------------------

Scott Cain, Ph. D. scott at

scottcain

dot
net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Ontario Institute for Cancer Research

--

------------------------------------------------------------------------

Scott Cain, Ph. D. scott at

scottcain dot

net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at
scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

[Scott Cain]

Hi Hufeng,

The only other thing I can think of is that apache isn't configured to process cgi scripts yet. That used to be on by default in most configurations, but that's becoming less common. Try this:

sudo a2enmod cgi

To turn it on.

Scott

Sent from my iPad

Thanks very much,
Yeah, indeed /usr/lib/cgi-bin exist as below.
total 348
-rwxr-xr-x 1 root root 35862 Nov 13 12:40 das
-rwxr-xr-x 1 root root 9232 Nov 13 12:40 gbgff
-rwxrwxrwx 1 root root 125875 Nov 13 12:40 gbrowse
-rwxr-xr-x 1 root root 15751 Nov 13 12:40 gbrowse_details
-rwxr-xr-x 1 root root 4562 Nov 13 12:40 gbrowse_est
-rwxr-xr-x 1 root root 35703 Nov 13 12:40 gbrowse_img
-rwxr-xr-x 1 root root 49935 Nov 13 12:40 gbrowse_moby
-rwxr-xr-x 1 root root 51716 Nov 13 12:40 gbrowse_syn
-rwxr-xr-x 1 root root 905 Nov 13 12:40 moby_server
-rwxr-xr-x 1 root root 4166 Sep 1 17:00 tutorial_test.pl
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Does /usr/lib/cgi-bin exist (which is where , and is the a file called gbrowse in it?

I find the precious package in /var/www/html/gbrowse/ was old one, didn't updated since my last installation in Oct.
So I did delete both /usr/local/apache or /usr/local/apache2 and /var/www/html/gbrowse/
And now I have unpack the GBrowse 1.70 and try the installation all from the very beginning, but the problem persists with the following history,
I still can't access the example data at http://localhost/cgi-bin/gbrowse/yeast
which always shows
The requested URL /cgi-bin/gbrowse/yeast was not found on this server.
Apache/2.4.7 (Ubuntu) Server at localhost Port 80
Should I use your previous settings to set the file paths and options (y/n) [y]? n
Apache root directory (enter '' for none)?
Apache conf directory? [/etc/apache2]
Apache htdocs directory? [/var/www/html]
Apache cgibin directory? [/usr/lib/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths
CONF /etc/apache2
HTDOCS /var/www/html
CGIBIN /usr/lib/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
Skip blib/lib/Bio/Graphics/Browser/I18n.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyBlock.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Realign.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm (unchanged)
Skip blib/lib/Bio/Graphics/DenseFeature.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/OptionPick.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PluginSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/allele_tower.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/GFFhelper.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/connector.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Markup.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Plugin.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PadAlignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PageSettings.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Synteny.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Util.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/UploadSet.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyIO.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/orf.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/ld_plot.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/phased_exons.pm (unchanged)
Skip blib/lib/CGI/Session/ID/salted_md5.pm (unchanged)
Skip blib/lib/Bio/Graphics/WiggleBlockFile.pm (unchanged)
Skip blib/lib/CGI/Toggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm (unchanged)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Skip ../blib/lib/Bio/Graphics/Browser/CAlign.pm (unchanged)
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.91 cusr 0.08 csys = 1.02 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/lib/cgi-bin/das
copying gbgff to /usr/lib/cgi-bin/gbgff
copying gbrowse to /usr/lib/cgi-bin/gbrowse
copying gbrowse_details to /usr/lib/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/lib/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/lib/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/lib/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/lib/cgi-bin/gbrowse_syn
copying moby_server to /usr/lib/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing stylesheet and images...
Making /var/www/html/gbrowse/images...
Making /var/www/html/gbrowse/images/buttons...
Making /var/www/html/gbrowse/images/balloons...
Making /var/www/html/gbrowse/js...
Making /var/www/html/gbrowse/images/help...
Installing temporary directory...
Making /var/www/html/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...
#############################################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Thanks very much, I deleted the /usr/local/apache2
but the problem persist, I still can not access the exemplary data here.
http://localhost/cgi-bin/gbrowse/yeast_chr1
Apache root directory (enter '' for none)? [/usr/local/apache] ''
Apache conf directory? [/usr/local/apache/conf]
Apache htdocs directory? [/usr/local/apache/htdocs]
Apache cgibin directory? [/usr/local/apache/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths
CONF /usr/local/apache/conf
HTDOCS /usr/local/apache/htdocs
CGIBIN /usr/local/apache/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp -typemap /usr/share/perl/5.18/ExtUtils/typemap CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 2 wallclock secs ( 0.03 usr 0.00 sys + 0.98 cusr 0.07 csys = 1.08 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man1/process_wormbase.pl.1p
Installing /usr/local/man/man1/make_das_conf.pl.1p
Installing /usr/local/man/man1/process_sgd.pl.1p
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache/cgi-bin/das
copying gbgff to /usr/local/apache/cgi-bin/gbgff
copying gbrowse to /usr/local/apache/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse" "CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin" "HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing stylesheet and images...
Making /usr/local/apache/htdocs/gbrowse/images...
Making /usr/local/apache/htdocs/gbrowse/images/buttons...
Making /usr/local/apache/htdocs/gbrowse/images/balloons...
Making /usr/local/apache/htdocs/gbrowse/js...
Making /usr/local/apache/htdocs/gbrowse/images/help...
Installing temporary directory...
Making /usr/local/apache/htdocs/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...
#############################################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

No--you want apache2. If you have the directory /usr/local/apache or /usr/local/apache2, delete it and reinstall GBrowse.

Thank you very much indeed for the indepth discussion and help, I am very grateful.
I actually installed apache2 on this machine already before I install GBrowse, shall I install apache version 1 instead now? If so, I will reinstall the apache version 1 and re-install GBrows now.
Our lab is very focus on the ChIA-PET data analysis and I have an independent Dell Power Edge server to use as my desktop for the ChIA-PET data analysis so it is not a webserver, but a dedicate powerful desktop. I use the Ubuntu distro version 14.10. I will try to install Apache1. at the moment.
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Do you have apache installed (or alternatively, did you try to install GBrowse once before you had apache installed)? The installer rather annoyingly assumes that if it doesn't find the "standard" locations for apache directories (which are also annoying different for different distros), it assumes that you must either have or be planning to have an apache server that you'll build yourself, which would go in /usr/local/apache2.
I can't tell from the output you sent what distro you're using, but I assume that you now have a webserver installed via the distro's package management software. Assuming that's true, you can delete the /usr/local/apache2 directory and then try to reinstall GBrowse. One thing I don't understand is how you have a gbrowse directory in /var/www given that the installer wants to install in /usr/local/apache2. The fact that there is also an html directory in /var/www makes me think that the htdocs directory for the installer should be /var/www/html, something that it will hopefully guess correctly after you remove the /usr/local/apache2 directory (though honestly, it may not, since, again, it's an old installer). If I knew what distro you were using, I could probably suggest the correct values for those items.
Scott

Thank you very much for your willingness to help.
it looks to be successfully installed, but I can't access the sample data and can't see the GBrowse visualize the genome,
http://localhost/cgi-bin/gbrowse/yeast_chr1
Here localhost/ is the directory on my server,/var/www/
total 8
drwxr-xr-x 10 root root 4096 Sep 1 17:00 gbrowse
drwxr-xr-x 4 root root 4096 Oct 24 17:05 html
but there is no cgi-bin in the directory /var/www/
only apach has in the following directory
/usr/local/apache2/cgi-bin
I am wondering if that is the causes of the issue?
So I need your help on this issue, thanks very much.
Here pasted the detail history of how I install the GBrowse1.70,
Apache root directory (enter '' for none)? [/usr/local/apache2]
Apache conf directory? [/usr/local/apache2/conf]
Apache htdocs directory? [/usr/local/apache2/htdocs]
Apache cgibin directory? [/usr/local/apache2/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths
CONF /usr/local/apache2/conf
HTDOCS /usr/local/apache2/htdocs
CGIBIN /usr/local/apache2/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/Synteny.pm blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/Graphics/DenseFeature.pm blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Realign.pm blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Browser/Markup.pm blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp -typemap /usr/share/perl/5.18/ExtUtils/typemap CAlign.xs > CAlign.xsc && mv CAlign.xsc CAlign.c
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/make_das_conf.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.95 cusr 0.03 csys = 1.01 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /usr/local/lib/perl/5.18.2/CGI/Toggle.pm
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man3/CGI::Toggle.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing /usr/local/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing /usr/local/bin/make_das_conf.pl
Installing /usr/local/bin/wiggle2gff3.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache2/cgi-bin/das
copying gbgff to /usr/local/apache2/cgi-bin/gbgff
copying gbrowse to /usr/local/apache2/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache2/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache2/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache2/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache2/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache2/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache2/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1" "HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin" "GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...
#############################################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Post by Hufeng Zhou
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.
But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
BioPerl and BioGraphics are two different things. I suspect BioPerl from
git will work fine, you must also install BioGraphics, most easily done with
cpan
cpan> install Bio::Graphics
Which will get you the most recent release of BioGraphics. Then you should
be able to install GBrowse 1.70, which is the most recent version of GBrowse
1 available (though that's still 5 years old).
I imagine the reason you want to use GBrowse 1 is because ChIA-PET creates a
GBrowse configuration file for you, which I suppose is some benefit as you
can't directly use a GBrowse 1 configuration file with GBrowse2. The data
that it generates is (I believe) compatible with GBrowse2 as well as JBrowse
(which is *much* easier to set up).
Scott

Thanks very much for your help.
I use this version of bioperl because,
Packaged versions of BioPerl contain a bug that prevents GBrowse from
displaying DNA sequences from in-memory databases. Install Bioperl
git clone https://github.com/bioperl/bioperl-live.git
cd bioperl-live
perl Build.PL
./Build test
sudo ./Build install
http://gmod.org/wiki/GBrowse_2.0_Prerequisites
And I find most of the bioperl version are quite old, may I know what
is the recommended version? I actually have some problem in installing
the latest version of bioperl but I forced to install the latest
version some how.
You can get the manual of ChiA-pet tool here.
http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Please keep this on the GBrowse mailing list (reply-all).
I don't understand why you haven't tried to update the version of
Bio::Graphics first, since the GBrowse installer asked you to install
it.
Can you point me to the documentation for ChiA-PET, because I have heard
of
people using ChiA-PET data with GBrowse2.
Scott

Thanks very much for your reply.
It is like this, I need to use a package called the ChiA-PET tool that
need to only use GBrowse version 1 (they mentioned on their manual,
version 2 won't work)
So I am trying to install the GBrowse version 1....
If I try to install Version 1.7
I will have following error
Installed Bio::Graphics version 1.654 is less than desired version 1.7.
You probably need to update your BioPerl to version 1.6 or better and
install Bio::Graphics separately from CPAN.
Died at Makefile.PL line 272, <DATA> line 192.
That is why I tried version. 1.66 it is the only package I can
install, but after I install it, I find version 1.66 can not even run
the example data.
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).
I really need your help on this.
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Sorry it took so long to get to this message; it was caught in the
spam
trap
that doesn't allow non-members to post to the list.
Is there a reason you aren't trying to install GBrowse2? GBrowse
1.66
is
extremely old. What were the problems you had?
If you really want to continue with 1.66, please look in the apache
access
log to see where apache is looking for the gbrowse cgi script, and
then
try
to find where it did get installed. Since distros are different with
regard
to where they put various files, it can be difficult for me to guess
where
they are. One possible suggestion that sometimes trips up new users
is
this: if you tried to install GBrowse before you installed apache,
the
GBrowse installer may have created a /usr/local/apache directory for
you.
If it did, I suggest you remove that directory and reinstall GBrowse.
Scott
On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou

Post by Hufeng Zhou
I have some problem with GBrowse, during the installation it has
some
errors so higher versions won't be able to install, I was only able
to
install GBrowse-1.66.
I can access http://localhost/gbrowse/ without any problems, and all
the
html pages can be viewed, the problem is in the welcome page, it
suggest me
to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example
data.
But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
accessed, which shows not found error.
I am wondering if it is GBrowse is not running? If there is any way
to
resolve this issue? Thanks very much.
After installation,
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/
------------------------------------------------------------------------------
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at
scottcain
dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

[Hufeng Zhou]

Dear Scott:
Thanks very much, yeah, it is not enabled previous,

so I enable that according to your suggestions as follows.

***@kiefflab-cloud:~$ sudo a2enmod cgi
[sudo] password for hufeng:
Enabling module cgi.
To activate the new configuration, you need to run:
service apache2 restart
***@kiefflab-cloud:~$ service apache2 restart
* Restarting web server
apache2
[fail]
***@kiefflab-cloud:~$ sudo a2enmod cgi
Module cgi already enabled
***@kiefflab-cloud:~$


It is already enabled.
But
http://localhost/cgi-bin/gbrowse/yeast
nor
http://localhost/cgi-bin/gbrowse/
nor
http://localhost/cgi-bin

can be accessed on the browser.

Sorry for so many problems,
If it is possible you can also access to my server through teamview, (ssh
access won't be possible. since the network is protected by the firewall.)


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
The only other thing I can think of is that apache isn't configured to
process cgi scripts yet. That used to be on by default in most
sudo a2enmod cgi
To turn it on.
Scott
Sent from my iPad
Thanks very much,
Yeah, indeed /usr/lib/cgi-bin exist as below.
/usr/lib/cgi-bin
total 348
-rwxr-xr-x 1 root root 35862 Nov 13 12:40 das
-rwxr-xr-x 1 root root 9232 Nov 13 12:40 gbgff
-rwxrwxrwx 1 root root 125875 Nov 13 12:40 gbrowse
-rwxr-xr-x 1 root root 15751 Nov 13 12:40 gbrowse_details
-rwxr-xr-x 1 root root 4562 Nov 13 12:40 gbrowse_est
-rwxr-xr-x 1 root root 35703 Nov 13 12:40 gbrowse_img
-rwxr-xr-x 1 root root 49935 Nov 13 12:40 gbrowse_moby
-rwxr-xr-x 1 root root 51716 Nov 13 12:40 gbrowse_syn
-rwxr-xr-x 1 root root 905 Nov 13 12:40 moby_server
-rwxr-xr-x 1 root root 4166 Sep 1 17:00 tutorial_test.pl
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Does /usr/lib/cgi-bin exist (which is where , and is the a file called gbrowse in it?

I find the precious package in /var/www/html/gbrowse/ was old one,
didn't updated since my last installation in Oct.
So I did delete both /usr/local/apache or /usr/local/apache2 and /var/www/html/gbrowse/
And now I have unpack the GBrowse 1.70 and try the installation all from
the very beginning, but the problem persists with the following history,
I still can't access the example data at
http://localhost/cgi-bin/gbrowse/yeast
which always shows
The requested URL /cgi-bin/gbrowse/yeast was not found on this server.
------------------------------
Apache/2.4.7 (Ubuntu) Server at localhost Port 80
Should I use your previous settings to set the file paths and options (y/n) [y]? n
Apache root directory (enter '' for none)?
Apache conf directory? [/etc/apache2]
Apache htdocs directory? [/var/www/html]
Apache cgibin directory? [/usr/lib/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths
CONF /etc/apache2
HTDOCS /var/www/html
CGIBIN /usr/lib/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
Skip blib/lib/Bio/Graphics/Browser/I18n.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyBlock.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Realign.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm (unchanged)
Skip blib/lib/Bio/Graphics/DenseFeature.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/OptionPick.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PluginSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/allele_tower.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/GFFhelper.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/connector.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Markup.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Plugin.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PadAlignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PageSettings.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Synteny.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Util.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/UploadSet.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyIO.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/orf.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/ld_plot.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/phased_exons.pm (unchanged)
Skip blib/lib/CGI/Session/ID/salted_md5.pm (unchanged)
Skip blib/lib/Bio/Graphics/WiggleBlockFile.pm (unchanged)
Skip blib/lib/CGI/Toggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm (unchanged)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Skip ../blib/lib/Bio/Graphics/Browser/CAlign.pm (unchanged)
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector
-fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\"
-fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/
process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/
process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/
make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/
wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS
bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
register_moby_services.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/
ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS
install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS
install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS
install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM"
"-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0,
'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.91 cusr
0.08 csys = 1.02 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture
dependent library tree
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
conf_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html"
"CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl"
"CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html" "CONF=/etc/apache2"
"GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/lib/cgi-bin/das
copying gbgff to /usr/lib/cgi-bin/gbgff
copying gbrowse to /usr/lib/cgi-bin/gbrowse
copying gbrowse_details to /usr/lib/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/lib/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/lib/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/lib/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/lib/cgi-bin/gbrowse_syn
copying moby_server to /usr/lib/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
htdocs_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html"
"CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing stylesheet and images...
Making /var/www/html/gbrowse/images...
Making /var/www/html/gbrowse/images/buttons...
Making /var/www/html/gbrowse/images/balloons...
Making /var/www/html/gbrowse/js...
Making /var/www/html/gbrowse/images/help...
Installing temporary directory...
Making /var/www/html/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...
#############################################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Thanks very much, I deleted the /usr/local/apache2
but the problem persist, I still can not access the exemplary data here.
http://localhost/cgi-bin/gbrowse/yeast_chr1
Apache root directory (enter '' for none)? [/usr/local/apache] ''
Apache conf directory? [/usr/local/apache/conf]
Apache htdocs directory? [/usr/local/apache/htdocs]
Apache cgibin directory? [/usr/local/apache/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths
CONF /usr/local/apache/conf
HTDOCS /usr/local/apache/htdocs
CGIBIN /usr/local/apache/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/
allele_tower.pm
cp lib/Bio/Graphics/Browser/Synteny.pm
blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm
blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm
blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm
blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/DenseFeature.pm
blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm
blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/I18n.pm
blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm
blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/
connector.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm
blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/Graphics/Browser/Realign.pm
blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/
orf.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm
blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/Graphics/Browser/Util.pm
blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm
blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm
blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm
blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm
blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Markup.pm
blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm
blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm
blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm
blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/
salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/
phased_exons.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm blib/lib/Bio/Graphics/Glyph/
pairwise_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm
blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/
ld_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm
blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm
blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp -typemap
/usr/share/perl/5.18/ExtUtils/typemap CAlign.xs > CAlign.xsc && mv
CAlign.xsc CAlign.c
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector
-fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\"
-fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/
wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/
process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS
bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/
make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/
process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_wormbase.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/
ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS
install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS
install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/gbrowse_ppm_install.PLS install_util/
gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM"
"-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0,
'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 2 wallclock secs ( 0.03 usr 0.00 sys + 0.98 cusr
0.07 csys = 1.08 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into
architecture dependent library tree
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man1/process_wormbase.pl.1p
Installing /usr/local/man/man1/make_das_conf.pl.1p
Installing /usr/local/man/man1/process_sgd.pl.1p
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
conf_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse"
"CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin"
"HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
cgi_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse"
"CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin"
"HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache/cgi-bin/das
copying gbgff to /usr/local/apache/cgi-bin/gbgff
copying gbrowse to /usr/local/apache/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
htdocs_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse"
"CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin"
"HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing stylesheet and images...
Making /usr/local/apache/htdocs/gbrowse/images...
Making /usr/local/apache/htdocs/gbrowse/images/buttons...
Making /usr/local/apache/htdocs/gbrowse/images/balloons...
Making /usr/local/apache/htdocs/gbrowse/js...
Making /usr/local/apache/htdocs/gbrowse/images/help...
Installing temporary directory...
Making /usr/local/apache/htdocs/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...
#############################################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Post by Scott Cain
No--you want apache2. If you have the directory /usr/local/apache or
/usr/local/apache2, delete it and reinstall GBrowse.
On Thu, Nov 13, 2014 at 12:00 PM, Hufeng Zhou <

Thank you very much indeed for the indepth discussion and help, I am
very grateful.
I actually installed apache2 on this machine already before I install
GBrowse, shall I install apache version 1 instead now? If so, I will
reinstall the apache version 1 and re-install GBrows now.
Our lab is very focus on the ChIA-PET data analysis and I have an
independent Dell Power Edge server to use as my desktop for the ChIA-PET
data analysis so it is not a webserver, but a dedicate powerful desktop. I
use the Ubuntu distro version 14.10. I will try to install Apache1. at the
moment.
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Do you have apache installed (or alternatively, did you try to
install GBrowse once before you had apache installed)? The installer
rather annoyingly assumes that if it doesn't find the "standard" locations
for apache directories (which are also annoying different for different
distros), it assumes that you must either have or be planning to have an
apache server that you'll build yourself, which would go in
/usr/local/apache2.
I can't tell from the output you sent what distro you're using, but
I assume that you now have a webserver installed via the distro's package
management software. Assuming that's true, you can delete the
/usr/local/apache2 directory and then try to reinstall GBrowse. One thing
I don't understand is how you have a gbrowse directory in /var/www given
that the installer wants to install in /usr/local/apache2. The fact that
there is also an html directory in /var/www makes me think that the htdocs
directory for the installer should be /var/www/html, something that it will
hopefully guess correctly after you remove the /usr/local/apache2 directory
(though honestly, it may not, since, again, it's an old installer). If I
knew what distro you were using, I could probably suggest the correct
values for those items.
Scott
On Wed, Nov 12, 2014 at 1:36 PM, Hufeng Zhou <

Thank you very much for your willingness to help.
it looks to be successfully installed, but I can't access the
sample data and can't see the GBrowse visualize the genome,
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1
Here localhost/ is the directory on my server,/var/www/
total 8
drwxr-xr-x 10 root root 4096 Sep 1 17:00 gbrowse
drwxr-xr-x 4 root root 4096 Oct 24 17:05 html
but there is no cgi-bin in the directory /var/www/
only apach has in the following directory
/usr/local/apache2/cgi-bin
I am wondering if that is the causes of the issue?
So I need your help on this issue, thanks very much.
Here pasted the detail history of how I install the GBrowse1.70,
Apache root directory (enter '' for none)? [/usr/local/apache2]
Apache conf directory? [/usr/local/apache2/conf]
Apache htdocs directory? [/usr/local/apache2/htdocs]
Apache cgibin directory? [/usr/local/apache2/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths
CONF /usr/local/apache2/conf
HTDOCS /usr/local/apache2/htdocs
CGIBIN /usr/local/apache2/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm
blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm
blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm
blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm
blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm
blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/Graphics/Glyph/allele_tower.pm
blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/Synteny.pm
blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/Graphics/DenseFeature.pm
blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm
blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/
orf.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Realign.pm
blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser/Util.pm
blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/
connector.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm
blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm
blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm
blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm
blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm
blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm
blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm
blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm
blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/I18n.pm
blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm
blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Browser/Markup.pm
blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm
blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm
blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm
blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/
salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm
blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/
ld_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm
blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp -typemap
/usr/share/perl/5.18/ExtUtils/typemap CAlign.xs > CAlign.xsc && mv
CAlign.xsc CAlign.c
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector
-fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\"
-fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/
process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/
wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable
substitutions)
cp bin/register_moby_services.pl blib/script/
register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS
bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/
make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
make_das_conf.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/
ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS
cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/gbrowse_ppm_install.PLS install_util/
gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM"
"-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0,
'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.95
cusr 0.03 csys = 1.01 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into
architecture dependent library tree
Installing /usr/local/lib/perl/5.18.2/CGI/Toggle.pm
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man3/CGI::Toggle.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing /usr/local/bin/make_das_conf.pl
Installing /usr/local/bin/wiggle2gff3.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
conf_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1"
"HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin"
"GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
cgi_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1"
"HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin"
"GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache2/cgi-bin/das
copying gbgff to /usr/local/apache2/cgi-bin/gbgff
copying gbrowse to /usr/local/apache2/cgi-bin/gbrowse
copying gbrowse_details to
/usr/local/apache2/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache2/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache2/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache2/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache2/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache2/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
htdocs_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1"
"HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin"
"GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement
path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement
path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...
#############################################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/
On Wed, Nov 12, 2014 at 1:23 PM, Hufeng Zhou <

Post by Hufeng Zhou
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.
But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
BioPerl and BioGraphics are two different things. I suspect

BioPerl from

git will work fine, you must also install BioGraphics, most

easily done with

cpan
cpan> install Bio::Graphics
Which will get you the most recent release of BioGraphics. Then

you should

be able to install GBrowse 1.70, which is the most recent

version of GBrowse

1 available (though that's still 5 years old).
I imagine the reason you want to use GBrowse 1 is because

ChIA-PET creates a

GBrowse configuration file for you, which I suppose is some

benefit as you

can't directly use a GBrowse 1 configuration file with

GBrowse2. The data

that it generates is (I believe) compatible with GBrowse2 as

well as JBrowse

(which is *much* easier to set up).
Scott
On Tue, Nov 11, 2014 at 5:08 PM, Hufeng Zhou <

Thanks very much for your help.
I use this version of bioperl because,
Packaged versions of BioPerl contain a bug that prevents

GBrowse from

displaying DNA sequences from in-memory databases. Install

Bioperl

git clone https://github.com/bioperl/bioperl-live.git
cd bioperl-live
perl Build.PL
./Build test
sudo ./Build install
http://gmod.org/wiki/GBrowse_2.0_Prerequisites
And I find most of the bioperl version are quite old, may I

know what

is the recommended version? I actually have some problem in

installing

the latest version of bioperl but I forced to install the latest
version some how.
You can get the manual of ChiA-pet tool here.
http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/
On Tue, Nov 11, 2014 at 3:10 PM, Scott Cain <

Hi Hufeng,
Please keep this on the GBrowse mailing list (reply-all).
I don't understand why you haven't tried to update the

version of

Bio::Graphics first, since the GBrowse installer asked you to

install

it.
Can you point me to the documentation for ChiA-PET, because I

have heard

of
people using ChiA-PET data with GBrowse2.
Scott
On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <

Thanks very much for your reply.
It is like this, I need to use a package called the ChiA-PET

tool that

need to only use GBrowse version 1 (they mentioned on their

manual,

version 2 won't work)
So I am trying to install the GBrowse version 1....
If I try to install Version 1.7
I will have following error
Installed Bio::Graphics version 1.654 is less than desired

version 1.7.

You probably need to update your BioPerl to version 1.6 or

better and

install Bio::Graphics separately from CPAN.
Died at Makefile.PL line 272, <DATA> line 192.
That is why I tried version. 1.66 it is the only package I

can

install, but after I install it, I find version 1.66 can not

even run

the example data.
An example in-memory database from yeast chromosome 1 has

been

http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be

accessed).

I really need your help on this.
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/
On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <

Hi Hufeng,
Sorry it took so long to get to this message; it was

caught in the

spam
trap
that doesn't allow non-members to post to the list.
Is there a reason you aren't trying to install GBrowse2?

GBrowse

1.66
is
extremely old. What were the problems you had?
If you really want to continue with 1.66, please look in

the apache

access
log to see where apache is looking for the gbrowse cgi

script, and

then
try
to find where it did get installed. Since distros are

different with

regard
to where they put various files, it can be difficult for

me to guess

where
they are. One possible suggestion that sometimes trips up

new users

is
this: if you tried to install GBrowse before you installed

apache,

the
GBrowse installer may have created a /usr/local/apache

directory for

you.
If it did, I suggest you remove that directory and

reinstall GBrowse.

Scott
On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou

Post by Hufeng Zhou
I have some problem with GBrowse, during the installation

it has

Post by Hufeng Zhou
some
errors so higher versions won't be able to install, I was

only able

Post by Hufeng Zhou
to
install GBrowse-1.66.
I can access http://localhost/gbrowse/ without any

problems, and all

Post by Hufeng Zhou
the
html pages can be viewed, the problem is in the welcome

page, it

Post by Hufeng Zhou
suggest me
to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for

the example

Post by Hufeng Zhou
data.
But this link http://localhost/cgi-bin/gbrowse/yeast_chr1

can not be

Post by Hufeng Zhou
accessed, which shows not found error.
I am wondering if it is GBrowse is not running? If there

is any way

Post by Hufeng Zhou
to
resolve this issue? Thanks very much.
After installation,
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

------------------------------------------------------------------------------

Post by Hufeng Zhou
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--

------------------------------------------------------------------------

Scott Cain, Ph. D. scott

at

scottcain
dot
net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Ontario Institute for Cancer Research

--

------------------------------------------------------------------------

Scott Cain, Ph. D. scott at

scottcain

dot
net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Ontario Institute for Cancer Research

--

------------------------------------------------------------------------

Scott Cain, Ph. D. scott at

scottcain dot

net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

[Hufeng Zhou]

Dear Scott:
I reinstall the GBrowse 1.7 but the problem still persists, do you think if
I reinstall apache2 would be better? or install apach1?

Here is the log of re-installation.

***@kiefflab-cloud:~/Programs/GBrowse$ sudo perl Makefile.PL
[sudo] password for hufeng:

Should I use your previous settings to set the file paths and options (y/n)
[y]? n
Apache root directory (enter '' for none)?
Apache conf directory? [/etc/apache2]
Apache htdocs directory? [/var/www/html]
Apache cgibin directory? [/usr/lib/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths

CONF /etc/apache2
HTDOCS /var/www/html
CGIBIN /usr/lib/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX

(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
***@kiefflab-cloud:~/Programs/GBrowse$ sudo make
Skip blib/lib/Bio/Graphics/Browser/OptionPick.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Synteny.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/connector.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PadAlignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Plugin.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PluginSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/GFFhelper.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/I18n.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteSet.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/orf.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PageSettings.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/UploadSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Realign.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyIO.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Markup.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyBlock.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/allele_tower.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Util.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm (unchanged)
Skip blib/lib/Bio/Graphics/DenseFeature.pm (unchanged)
Skip blib/lib/Bio/Graphics/WiggleBlockFile.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/phased_exons.pm (unchanged)
Skip blib/lib/CGI/Session/ID/salted_md5.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/ld_plot.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm (unchanged)
Skip blib/lib/CGI/Toggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm (unchanged)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Skip ../blib/lib/Bio/Graphics/Browser/CAlign.pm (unchanged)
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector
-fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\"
-fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\

chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/
make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/
process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/
process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/
wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS bin/
register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
register_moby_services.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/
ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS
cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS
install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS
install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/gbrowse_ppm_install.PLS install_util/gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/htdocs_install.PLS
install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
***@kiefflab-cloud:~/Programs/GBrowse$ sudo make test
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness"
"-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib',
'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 1 wallclock secs ( 0.03 usr 0.01 sys + 0.98 cusr
0.02 csys = 1.04 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
***@kiefflab-cloud:~/Programs/GBrowse$ vim INSTALL
***@kiefflab-cloud:~/Programs/GBrowse$ make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Can't create cgi-bin/gbrowse: Permission denied at cgi-bin/gbrowse.PLS line
26.
make: *** [cgi-bin/gbrowse] Error 13
***@kiefflab-cloud:~/Programs/GBrowse$ sudo make install UNINST=1
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into architecture
dependent library tree
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man1/process_wormbase.pl.1p
Installing /usr/local/man/man1/make_das_conf.pl.1p
Installing /usr/local/man/man1/process_sgd.pl.1p
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/conf_install.pl"
"CONF=/etc/apache2" "DO_XS=1" "CGIBIN=/usr/lib/cgi-bin"
"HTDOCS=/var/www/html" "GBROWSE_ROOT=gbrowse" "APACHE=/"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/cgi_install.pl"
"CONF=/etc/apache2" "DO_XS=1" "CGIBIN=/usr/lib/cgi-bin"
"HTDOCS=/var/www/html" "GBROWSE_ROOT=gbrowse" "APACHE=/"
Installing gbrowse CGI scripts...
copying das to /usr/lib/cgi-bin/das
copying gbgff to /usr/lib/cgi-bin/gbgff
copying gbrowse to /usr/lib/cgi-bin/gbrowse
copying gbrowse_details to /usr/lib/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/lib/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/lib/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/lib/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/lib/cgi-bin/gbrowse_syn
copying moby_server to /usr/lib/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/htdocs_install.pl"
"CONF=/etc/apache2" "DO_XS=1" "CGIBIN=/usr/lib/cgi-bin"
"HTDOCS=/var/www/html" "GBROWSE_ROOT=gbrowse" "APACHE=/"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...


#############################################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Post by Hufeng Zhou
Thanks very much, yeah, it is not enabled previous,
so I enable that according to your suggestions as follows.
Enabling module cgi.
service apache2 restart
* Restarting web server
apache2
[fail]
Module cgi already enabled
It is already enabled.
But
http://localhost/cgi-bin/gbrowse/yeast
nor
http://localhost/cgi-bin/gbrowse/
nor
http://localhost/cgi-bin
can be accessed on the browser.
Sorry for so many problems,
If it is possible you can also access to my server through teamview, (ssh
access won't be possible. since the network is protected by the firewall.)
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
The only other thing I can think of is that apache isn't configured to
process cgi scripts yet. That used to be on by default in most
sudo a2enmod cgi
To turn it on.
Scott
Sent from my iPad
Thanks very much,
Yeah, indeed /usr/lib/cgi-bin exist as below.
total 348
-rwxr-xr-x 1 root root 35862 Nov 13 12:40 das
-rwxr-xr-x 1 root root 9232 Nov 13 12:40 gbgff
-rwxrwxrwx 1 root root 125875 Nov 13 12:40 gbrowse
-rwxr-xr-x 1 root root 15751 Nov 13 12:40 gbrowse_details
-rwxr-xr-x 1 root root 4562 Nov 13 12:40 gbrowse_est
-rwxr-xr-x 1 root root 35703 Nov 13 12:40 gbrowse_img
-rwxr-xr-x 1 root root 49935 Nov 13 12:40 gbrowse_moby
-rwxr-xr-x 1 root root 51716 Nov 13 12:40 gbrowse_syn
-rwxr-xr-x 1 root root 905 Nov 13 12:40 moby_server
-rwxr-xr-x 1 root root 4166 Sep 1 17:00 tutorial_test.pl
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Does /usr/lib/cgi-bin exist (which is where , and is the a file called gbrowse in it?

I find the precious package in /var/www/html/gbrowse/ was old one,
didn't updated since my last installation in Oct.
So I did delete both /usr/local/apache or /usr/local/apache2 and
/var/www/html/gbrowse/
And now I have unpack the GBrowse 1.70 and try the installation all
from the very beginning, but the problem persists with the following
history,
I still can't access the example data at
http://localhost/cgi-bin/gbrowse/yeast
which always shows
The requested URL /cgi-bin/gbrowse/yeast was not found on this server.
------------------------------
Apache/2.4.7 (Ubuntu) Server at localhost Port 80
Should I use your previous settings to set the file paths and options (y/n) [y]? n
Apache root directory (enter '' for none)?
Apache conf directory? [/etc/apache2]
Apache htdocs directory? [/var/www/html]
Apache cgibin directory? [/usr/lib/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths
CONF /etc/apache2
HTDOCS /var/www/html
CGIBIN /usr/lib/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
Skip blib/lib/Bio/Graphics/Browser/I18n.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyBlock.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Realign.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm (unchanged)
Skip blib/lib/Bio/Graphics/DenseFeature.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/OptionPick.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PluginSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/allele_tower.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/GFFhelper.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/connector.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/RemoteSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Markup.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Plugin.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/ConfigSet.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PadAlignment.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/PageSettings.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Synteny.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/Util.pm (unchanged)
Skip blib/lib/Bio/Graphics/Browser/UploadSet.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/SyntenyIO.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm (unchanged)
Skip blib/lib/Bio/DB/GFF/Aggregator/orf.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/ld_plot.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/phased_exons.pm (unchanged)
Skip blib/lib/CGI/Session/ID/salted_md5.pm (unchanged)
Skip blib/lib/Bio/Graphics/WiggleBlockFile.pm (unchanged)
Skip blib/lib/CGI/Toggle.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm (unchanged)
Skip blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm (unchanged)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Skip ../blib/lib/Bio/Graphics/Browser/CAlign.pm (unchanged)
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector
-fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\"
-fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/
process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/
process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/
make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/
wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/register_moby_services.PLS
bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
register_moby_services.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/
ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS
install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS
install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/gbrowse_ppm_install.PLS install_util/
gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM"
"-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0,
'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.91 cusr
0.08 csys = 1.02 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into
architecture dependent library tree
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
conf_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html"
"CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
cgi_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html"
"CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/lib/cgi-bin/das
copying gbgff to /usr/lib/cgi-bin/gbgff
copying gbrowse to /usr/lib/cgi-bin/gbrowse
copying gbrowse_details to /usr/lib/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/lib/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/lib/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/lib/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/lib/cgi-bin/gbrowse_syn
copying moby_server to /usr/lib/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
htdocs_install.pl" "CGIBIN=/usr/lib/cgi-bin" "HTDOCS=/var/www/html"
"CONF=/etc/apache2" "GBROWSE_ROOT=gbrowse" "APACHE=/" "DO_XS=1"
Installing stylesheet and images...
Making /var/www/html/gbrowse/images...
Making /var/www/html/gbrowse/images/buttons...
Making /var/www/html/gbrowse/images/balloons...
Making /var/www/html/gbrowse/js...
Making /var/www/html/gbrowse/images/help...
Installing temporary directory...
Making /var/www/html/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...
#############################################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Thanks very much, I deleted the /usr/local/apache2
but the problem persist, I still can not access the exemplary data here.
http://localhost/cgi-bin/gbrowse/yeast_chr1
Apache root directory (enter '' for none)? [/usr/local/apache] ''
Apache conf directory? [/usr/local/apache/conf]
Apache htdocs directory? [/usr/local/apache/htdocs]
Apache cgibin directory? [/usr/local/apache/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths
CONF /usr/local/apache/conf
HTDOCS /usr/local/apache/htdocs
CGIBIN /usr/local/apache/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
cp lib/Bio/Graphics/Glyph/allele_tower.pm blib/lib/Bio/Graphics/Glyph/
allele_tower.pm
cp lib/Bio/Graphics/Browser/Synteny.pm
blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm
blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm
blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm
blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/DenseFeature.pm
blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm
blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/I18n.pm
blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm
blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Glyph/connector.pm blib/lib/Bio/Graphics/Glyph/
connector.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm
blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/Graphics/Browser/Realign.pm
blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/
orf.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm
blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/Graphics/Browser/Util.pm
blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm
blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm
blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm
blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm
blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Markup.pm
blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm
blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm
blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm
blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/
salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm blib/lib/Bio/Graphics/Glyph/
phased_exons.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm
blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm
blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/
ld_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm
blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm
blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp -typemap
/usr/share/perl/5.18/ExtUtils/typemap CAlign.xs > CAlign.xsc && mv
CAlign.xsc CAlign.c
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector
-fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\"
-fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- CAlign.bs
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/
wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/
process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/
make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
make_das_conf.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS bin/
process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_wormbase.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS bin/
ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS
cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS
cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/cgi_install.PLS
install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" install_util/conf_install.PLS
install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/gbrowse_ppm_install.PLS install_util/
gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM"
"-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0,
'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 2 wallclock secs ( 0.03 usr 0.00 sys + 0.98
cusr 0.07 csys = 1.08 CPU)
Result: PASS
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Entering directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_details.PLS
cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into
architecture dependent library tree
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man1/process_wormbase.pl.1p
Installing /usr/local/man/man1/make_das_conf.pl.1p
Installing /usr/local/man/man1/process_sgd.pl.1p
Installing /usr/local/bin/register_moby_services.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
conf_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse"
"CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin"
"HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
cgi_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse"
"CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin"
"HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache/cgi-bin/das
copying gbgff to /usr/local/apache/cgi-bin/gbgff
copying gbrowse to /usr/local/apache/cgi-bin/gbrowse
copying gbrowse_details to /usr/local/apache/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
htdocs_install.pl" "APACHE=''" "GBROWSE_ROOT=gbrowse"
"CONF=/usr/local/apache/conf" "CGIBIN=/usr/local/apache/cgi-bin"
"HTDOCS=/usr/local/apache/htdocs" "DO_XS=1"
Installing stylesheet and images...
Making /usr/local/apache/htdocs/gbrowse/images...
Making /usr/local/apache/htdocs/gbrowse/images/buttons...
Making /usr/local/apache/htdocs/gbrowse/images/balloons...
Making /usr/local/apache/htdocs/gbrowse/js...
Making /usr/local/apache/htdocs/gbrowse/images/help...
Installing temporary directory...
Making /usr/local/apache/htdocs/gbrowse/tmp...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement path,
cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...
#############################################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and reference manual.
#############################################################################
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Post by Scott Cain
No--you want apache2. If you have the directory /usr/local/apache or
/usr/local/apache2, delete it and reinstall GBrowse.
On Thu, Nov 13, 2014 at 12:00 PM, Hufeng Zhou <

Thank you very much indeed for the indepth discussion and help, I am
very grateful.
I actually installed apache2 on this machine already before I
install GBrowse, shall I install apache version 1 instead now? If so, I
will reinstall the apache version 1 and re-install GBrows now.
Our lab is very focus on the ChIA-PET data analysis and I have an
independent Dell Power Edge server to use as my desktop for the ChIA-PET
data analysis so it is not a webserver, but a dedicate powerful desktop. I
use the Ubuntu distro version 14.10. I will try to install Apache1. at the
moment.
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
Do you have apache installed (or alternatively, did you try to
install GBrowse once before you had apache installed)? The installer
rather annoyingly assumes that if it doesn't find the "standard" locations
for apache directories (which are also annoying different for different
distros), it assumes that you must either have or be planning to have an
apache server that you'll build yourself, which would go in
/usr/local/apache2.
I can't tell from the output you sent what distro you're using, but
I assume that you now have a webserver installed via the distro's package
management software. Assuming that's true, you can delete the
/usr/local/apache2 directory and then try to reinstall GBrowse. One thing
I don't understand is how you have a gbrowse directory in /var/www given
that the installer wants to install in /usr/local/apache2. The fact that
there is also an html directory in /var/www makes me think that the htdocs
directory for the installer should be /var/www/html, something that it will
hopefully guess correctly after you remove the /usr/local/apache2 directory
(though honestly, it may not, since, again, it's an old installer). If I
knew what distro you were using, I could probably suggest the correct
values for those items.
Scott
On Wed, Nov 12, 2014 at 1:36 PM, Hufeng Zhou <

Thank you very much for your willingness to help.
it looks to be successfully installed, but I can't access the
sample data and can't see the GBrowse visualize the genome,
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1
Here localhost/ is the directory on my server,/var/www/
total 8
drwxr-xr-x 10 root root 4096 Sep 1 17:00 gbrowse
drwxr-xr-x 4 root root 4096 Oct 24 17:05 html
but there is no cgi-bin in the directory /var/www/
only apach has in the following directory
/usr/local/apache2/cgi-bin
I am wondering if that is the causes of the issue?
So I need your help on this issue, thanks very much.
Here pasted the detail history of how I install the GBrowse1.70,
Apache root directory (enter '' for none)? [/usr/local/apache2]
Apache conf directory? [/usr/local/apache2/conf]
Apache htdocs directory? [/usr/local/apache2/htdocs]
Apache cgibin directory? [/usr/local/apache2/cgi-bin]
GBrowse root for static files? [gbrowse]
----------------------------------------------
File Paths
CONF /usr/local/apache2/conf
HTDOCS /usr/local/apache2/htdocs
CGIBIN /usr/local/apache2/cgi-bin
GBROWSE_ROOT gbrowse
INSTALL_BASE
LIB
BIN
YES
PREFIX
PACKAGE_DIR
DO_XS 1
NONROOT
SELINUX
(Run perl Makefile.PL -h for help on changing)
----------------------------------------------
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Perl 1.006 not found. We have unknown version.
Warning: NAME must be a package name
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Graphics::Browser::CAlign
Writing MYMETA.yml and MYMETA.json
Generating a Unix-style Makefile
Writing Makefile for Generic-Genome-Browser
Writing MYMETA.yml and MYMETA.json
cp lib/Bio/Graphics/Glyph/genscan_transcript.pm
blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
cp lib/Bio/Graphics/Browser/RemoteSet.pm
blib/lib/Bio/Graphics/Browser/RemoteSet.pm
cp lib/Bio/Graphics/Browser/Plugin.pm
blib/lib/Bio/Graphics/Browser/Plugin.pm
cp lib/Bio/Graphics/Browser/PluginSet.pm
blib/lib/Bio/Graphics/Browser/PluginSet.pm
cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm
blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
cp lib/Bio/Graphics/Glyph/allele_tower.pm
blib/lib/Bio/Graphics/Glyph/allele_tower.pm
cp lib/Bio/DB/GFF/SyntenyIO.pm blib/lib/Bio/DB/GFF/SyntenyIO.pm
cp lib/Bio/Graphics/Browser/Synteny.pm
blib/lib/Bio/Graphics/Browser/Synteny.pm
cp lib/Bio/Graphics/DenseFeature.pm
blib/lib/Bio/Graphics/DenseFeature.pm
cp lib/Bio/Graphics/Browser/PageSettings.pm
blib/lib/Bio/Graphics/Browser/PageSettings.pm
cp lib/Bio/DB/GFF/Aggregator/orf.pm
blib/lib/Bio/DB/GFF/Aggregator/orf.pm
cp lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/quantitative.pm
cp lib/Bio/Graphics/Browser/Realign.pm
blib/lib/Bio/Graphics/Browser/Realign.pm
cp lib/Bio/Graphics/Browser/Util.pm
blib/lib/Bio/Graphics/Browser/Util.pm
cp lib/Bio/Graphics/Glyph/connector.pm
blib/lib/Bio/Graphics/Glyph/connector.pm
cp lib/Bio/Graphics/Browser/GFFhelper.pm
blib/lib/Bio/Graphics/Browser/GFFhelper.pm
cp lib/Bio/Graphics/Browser/RemoteDataBase.pm
blib/lib/Bio/Graphics/Browser/RemoteDataBase.pm
cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm
blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
cp lib/Bio/Graphics/Browser/UploadSet.pm
blib/lib/Bio/Graphics/Browser/UploadSet.pm
cp lib/Bio/DB/GFF/SyntenyBlock.pm
blib/lib/Bio/DB/GFF/SyntenyBlock.pm
cp lib/Bio/Graphics/Browser/PadAlignment.pm
blib/lib/Bio/Graphics/Browser/PadAlignment.pm
cp lib/Bio/Graphics/Browser/OptionPick.pm
blib/lib/Bio/Graphics/Browser/OptionPick.pm
cp lib/Bio/Graphics/Browser/ConfigSet.pm
blib/lib/Bio/Graphics/Browser/ConfigSet.pm
cp lib/Bio/Graphics/Browser/I18n.pm
blib/lib/Bio/Graphics/Browser/I18n.pm
cp lib/Bio/DB/GFF/Aggregator/match_gap.pm
blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
cp lib/Bio/Graphics/Browser/ConfigSet/basic.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/basic.pm
cp lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
blib/lib/Bio/Graphics/Browser/ConfigSet/wiggle.pm
cp lib/Bio/Graphics/Browser/Markup.pm
blib/lib/Bio/Graphics/Browser/Markup.pm
cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm
blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
cp lib/Bio/Graphics/Glyph/pairwise_plot.pm
blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
cp lib/Bio/Graphics/WiggleBlockFile.pm
blib/lib/Bio/Graphics/WiggleBlockFile.pm
cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/
salted_md5.pm
cp lib/Bio/Graphics/Glyph/phased_exons.pm
blib/lib/Bio/Graphics/Glyph/phased_exons.pm
cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/
ld_plot.pm
cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm
blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
make[1]: Entering directory
`/home/hufeng/Programs/GBrowse/libalign'
cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
/usr/bin/perl /usr/share/perl/5.18.2/ExtUtils/xsubpp -typemap
/usr/share/perl/5.18/ExtUtils/typemap CAlign.xs > CAlign.xsc && mv
CAlign.xsc CAlign.c
cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fstack-protector
-fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\"
-fPIC "-I/usr/lib/perl/5.18/CORE" CAlign.c
rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
cc -shared -L/usr/local/lib -fstack-protector CAlign.o -o
../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
\
chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' --
CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs 644
Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_sgd.PLS bin/
process_sgd.pl
Extracting process_sgd.pl (with variable substitutions)
cp bin/process_sgd.pl blib/script/process_sgd.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_sgd.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/wiggle2gff3.PLS bin/
wiggle2gff3.pl
Extracting wiggle2gff3.pl (with variable substitutions)
cp bin/wiggle2gff3.pl blib/script/wiggle2gff3.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
wiggle2gff3.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
bin/register_moby_services.PLS bin/register_moby_services.pl
Extracting bin/register_moby_services.pl (with variable substitutions)
cp bin/register_moby_services.pl blib/script/
register_moby_services.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
register_moby_services.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/process_wormbase.PLS
bin/process_wormbase.pl
Extracting process_wormbase.pl (with variable substitutions)
cp bin/process_wormbase.pl blib/script/process_wormbase.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
process_wormbase.pl
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/make_das_conf.PLS bin/
make_das_conf.pl
Extracting make_das_conf.pl (with variable substitutions)
cp bin/make_das_conf.pl blib/script/make_das_conf.pl
/usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/
make_das_conf.pl
Manifying blib/man1/make_das_conf.pl.1p
Manifying blib/man1/process_sgd.pl.1p
Manifying blib/man1/process_wormbase.pl.1p
Manifying blib/man1/register_moby_services.pl.1p
Manifying blib/man1/wiggle2gff3.pl.1p
Manifying blib/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::orf.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Manifying blib/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Manifying blib/man3/Bio::Graphics::Browser.3pm
Manifying blib/man3/Bio::Graphics::Browser::ConfigSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::GFFhelper.3pm
Manifying blib/man3/Bio::Graphics::Browser::Markup.3pm
Manifying blib/man3/Bio::Graphics::Browser::OptionPick.3pm
Manifying blib/man3/Bio::Graphics::Browser::PadAlignment.3pm
Manifying blib/man3/Bio::Graphics::Browser::Plugin.3pm
Manifying blib/man3/Bio::Graphics::Browser::PluginSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Realign.3pm
Manifying blib/man3/Bio::Graphics::Browser::RemoteSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::UploadSet.3pm
Manifying blib/man3/Bio::Graphics::Browser::Util.3pm
Manifying blib/man3/Bio::Graphics::DenseFeature.3pm
Manifying blib/man3/Bio::Graphics::Glyph::allele_tower.3pm
Manifying blib/man3/Bio::Graphics::Glyph::genscan_transcript.3pm
Manifying blib/man3/Bio::Graphics::Glyph::insertion_chromosome.3pm
Manifying blib/man3/Bio::Graphics::Glyph::ld_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::pairwise_plot.3pm
Manifying blib/man3/Bio::Graphics::Glyph::wormbase_transcript.3pm
Manifying blib/man3/Bio::Graphics::WiggleBlockFile.3pm
Manifying blib/man3/CGI::Session::ID::salted_md5.3pm
Manifying blib/man3/CGI::Toggle.3pm
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" bin/ucsc_genes2gff.PLS
bin/ucsc_genes2gff.pl
Extracting ucsc_genes2gff.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/das.PLS cgi-bin/das
Extracting cgi-bin/das (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbgff.PLS cgi-bin/gbgff
Extracting cgi-bin/gbgff (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/moby_server.PLS
cgi-bin/moby_server
Extracting MOBY cgi-bin/moby_server (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
conf/MobyServices/GbrowseServices.PMS conf/MobyServices/GbrowseServices.pm
Extracting conf/MobyServices/GbrowseServices.pm (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/cgi_install.PLS install_util/cgi_install.pl
Extracting cgi_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/conf_install.PLS install_util/conf_install.pl
Extracting conf_install.pl (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/gbrowse_ppm_install.PLS install_util/
gbrowse_ppm_install.pl
Extracting install_util/gbrowse_ppm_install.pl (with variable
substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
install_util/htdocs_install.PLS install_util/htdocs_install.pl
Extracting htdocs_install.pl (with variable substitutions)
make[1]: Entering directory
`/home/hufeng/Programs/GBrowse/libalign'
Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
chmod 644 CAlign.bs
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM"
"-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0,
'blib/lib', 'blib/arch')" t/*.t
t/01yeast.t ........ ok
t/02.wiggle.t ...... ok
t/GBrowse_Chado.t .. ok
All tests successful.
Files=3, Tests=61, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.95
cusr 0.03 csys = 1.01 CPU)
Result: PASS
make[1]: Entering directory
`/home/hufeng/Programs/GBrowse/libalign'
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl
1..3
ok 1
ok 2
ok 3
ok 4
ok 5
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
make[1]: Entering directory
`/home/hufeng/Programs/GBrowse/libalign'
make[1]: Leaving directory `/home/hufeng/Programs/GBrowse/libalign'
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS
cgi-bin/gbrowse
Extracting cgi-bin/gbrowse (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib"
cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details
Extracting cgi-bin/gbrowse_details (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS
cgi-bin/gbrowse_est
Extracting cgi-bin/gbrowse_est (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS
cgi-bin/gbrowse_img
Extracting cgi-bin/gbrowse_img (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS
cgi-bin/gbrowse_moby
Extracting cgi-bin/gbrowse_moby (with variable substitutions)
/usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS
cgi-bin/gbrowse_syn
Extracting cgi-bin/gbrowse_syn (with variable substitutions)
Files found in blib/arch: installing files in blib/lib into
architecture dependent library tree
Installing /usr/local/lib/perl/5.18.2/CGI/Toggle.pm
Installing /usr/local/man/man1/wiggle2gff3.pl.1p
Installing /usr/local/man/man3/CGI::Toggle.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::waba_alignment.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::match_gap.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::reftranscript.3pm
Installing
/usr/local/man/man3/Bio::DB::GFF::Aggregator::wormbase_gene.3pm
Installing /usr/local/bin/make_das_conf.pl
Installing /usr/local/bin/wiggle2gff3.pl
Appending installation info to /usr/lib/perl/5.18/perllocal.pod
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
conf_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1"
"HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin"
"GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing sample configuration files...
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
cgi_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1"
"HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin"
"GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing gbrowse CGI scripts...
copying das to /usr/local/apache2/cgi-bin/das
copying gbgff to /usr/local/apache2/cgi-bin/gbgff
copying gbrowse to /usr/local/apache2/cgi-bin/gbrowse
copying gbrowse_details to
/usr/local/apache2/cgi-bin/gbrowse_details
copying gbrowse_est to /usr/local/apache2/cgi-bin/gbrowse_est
copying gbrowse_img to /usr/local/apache2/cgi-bin/gbrowse_img
copying gbrowse_moby to /usr/local/apache2/cgi-bin/gbrowse_moby
copying gbrowse_syn to /usr/local/apache2/cgi-bin/gbrowse_syn
copying moby_server to /usr/local/apache2/cgi-bin/moby_server
/usr/bin/perl "/home/hufeng/Programs/GBrowse/install_util/
htdocs_install.pl" "CONF=/usr/local/apache2/conf" "DO_XS=1"
"HTDOCS=/usr/local/apache2/htdocs" "CGIBIN=/usr/local/apache2/cgi-bin"
"GBROWSE_ROOT=gbrowse" "APACHE=/usr/local/apache2"
Installing stylesheet and images...
Installing temporary directory...
Installing documentation...
Cannot find "ftp:" in podpath: cannot find suitable replacement
path, cannot resolve link
Cannot find "ftp:" in podpath: cannot find suitable replacement
path, cannot resolve link
Installing tutorial...
Installing contrib...
Installing js files...
Installing sample data files...
#############################################################################
GBrowse is now installed. Read INSTALL for further setup instructions.
Go to http://localhost/gbrowse for the online tutorial and
reference manual.
#############################################################################
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/
On Wed, Nov 12, 2014 at 1:23 PM, Hufeng Zhou <

Post by Hufeng Zhou
Thanks very much.
Yeah indeed, ChIA-PET configuration file works only with the version
1, the tool itself it is also 5 years old.
Use your valuable suggestions, I did upgrade the Bio::Graphiscs and
the installation of Gbrowse1.70 seems to be very good.
But I still can't access the following sample data.
An example in-memory database from yeast chromosome 1 has been
http://localhost/cgi-bin/gbrowse/yeast_chr1
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

Hi Hufeng,
BioPerl and BioGraphics are two different things. I suspect

BioPerl from

git will work fine, you must also install BioGraphics, most

easily done with

cpan
cpan> install Bio::Graphics
Which will get you the most recent release of BioGraphics.

Then you should

be able to install GBrowse 1.70, which is the most recent

version of GBrowse

1 available (though that's still 5 years old).
I imagine the reason you want to use GBrowse 1 is because

ChIA-PET creates a

GBrowse configuration file for you, which I suppose is some

benefit as you

can't directly use a GBrowse 1 configuration file with

GBrowse2. The data

that it generates is (I believe) compatible with GBrowse2 as

well as JBrowse

(which is *much* easier to set up).
Scott
On Tue, Nov 11, 2014 at 5:08 PM, Hufeng Zhou <

Thanks very much for your help.
I use this version of bioperl because,
Packaged versions of BioPerl contain a bug that prevents

GBrowse from

displaying DNA sequences from in-memory databases. Install

Bioperl

git clone https://github.com/bioperl/bioperl-live.git
cd bioperl-live
perl Build.PL
./Build test
sudo ./Build install
http://gmod.org/wiki/GBrowse_2.0_Prerequisites
And I find most of the bioperl version are quite old, may I

know what

is the recommended version? I actually have some problem in

installing

the latest version of bioperl but I forced to install the

latest

version some how.
You can get the manual of ChiA-pet tool here.
http://chiapet.gis.a-star.edu.sg/downloads/chia-pet-tools
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/
On Tue, Nov 11, 2014 at 3:10 PM, Scott Cain <

Hi Hufeng,
Please keep this on the GBrowse mailing list (reply-all).
I don't understand why you haven't tried to update the

version of

Bio::Graphics first, since the GBrowse installer asked you

to install

it.
Can you point me to the documentation for ChiA-PET, because

I have heard

of
people using ChiA-PET data with GBrowse2.
Scott
On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <

Thanks very much for your reply.
It is like this, I need to use a package called the

ChiA-PET tool that

need to only use GBrowse version 1 (they mentioned on their

manual,

version 2 won't work)
So I am trying to install the GBrowse version 1....
If I try to install Version 1.7
I will have following error
Installed Bio::Graphics version 1.654 is less than desired

version 1.7.

You probably need to update your BioPerl to version 1.6 or

better and

install Bio::Graphics separately from CPAN.
Died at Makefile.PL line 272, <DATA> line 192.
That is why I tried version. 1.66 it is the only package I

can

install, but after I install it, I find version 1.66 can

not even run

the example data.
An example in-memory database from yeast chromosome 1 has

been

http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't

be accessed).

I really need your help on this.
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/
On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <

Hi Hufeng,
Sorry it took so long to get to this message; it was

caught in the

spam
trap
that doesn't allow non-members to post to the list.
Is there a reason you aren't trying to install GBrowse2?

GBrowse

1.66
is
extremely old. What were the problems you had?
If you really want to continue with 1.66, please look in

the apache

access
log to see where apache is looking for the gbrowse cgi

script, and

then
try
to find where it did get installed. Since distros are

different with

regard
to where they put various files, it can be difficult for

me to guess

where
they are. One possible suggestion that sometimes trips

up new users

is
this: if you tried to install GBrowse before you

installed apache,

the
GBrowse installer may have created a /usr/local/apache

directory for

you.
If it did, I suggest you remove that directory and

reinstall GBrowse.

Scott
On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou

Post by Hufeng Zhou
I have some problem with GBrowse, during the

installation it has

Post by Hufeng Zhou
some
errors so higher versions won't be able to install, I

was only able

Post by Hufeng Zhou
to
install GBrowse-1.66.
I can access http://localhost/gbrowse/ without any

problems, and all

Post by Hufeng Zhou
the
html pages can be viewed, the problem is in the welcome

page, it

Post by Hufeng Zhou
suggest me
to visit http://localhost/cgi-bin/gbrowse/yeast_chr1

for the example

Post by Hufeng Zhou
data.
But this link

http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be

Post by Hufeng Zhou
accessed, which shows not found error.
I am wondering if it is GBrowse is not running? If there

is any way

Post by Hufeng Zhou
to
resolve this issue? Thanks very much.
After installation,
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone: [phone]
Website: kiefflab.hms.harvard.edu/zhouhufeng/

------------------------------------------------------------------------------

Post by Hufeng Zhou
_______________________________________________
Gmod-gbrowse mailing list

https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--

------------------------------------------------------------------------

Scott Cain, Ph. D.

scott at

scottcain
dot
net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Ontario Institute for Cancer Research

--

------------------------------------------------------------------------

Scott Cain, Ph. D. scott

at scottcain

dot
net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Ontario Institute for Cancer Research

--

------------------------------------------------------------------------

Scott Cain, Ph. D. scott at

scottcain dot

net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at
scottcain dot net
GMOD Coordinator (http://gmod.org/)
216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research